Help Contents
Contents

What's New in 4.5

Introduction

Chapter 1, ChemDraw Basics

Chapter 2, Getting Started Tutorials

Chapter 3, Drawing Chemical Structures

Chapter 4, Captions and Atom Labels

Chapter 5, Drawing Orbitals and Chemical Symbols

Chapter 6, Drawing Arrows, Arcs and Other Shapes

Chapter 7, Working with Selections

Chapter 8, Advanced Drawing Techniques

Chapter 9, Drawing Query Structures

Chapter 10, Drawing With Templates

Chapter 11, Reactions

Chapter 12, Working with Page Layout

Chapter 13, Sharing Information

Appendix A, The Chemistry of ChemDraw

Appendix B, Specifying Paths

Appendix C, Technical Support

Appendix D, Document Settings

Appendix E, Apple Events (Macintosh)

Appendix F, Chemistry File Formats


Introduction

Overview

About this Help File

Organization of this help file

Conventions

Getting Additional Help

Installation/System Requirements


Chapter 1, ChemDraw Basics

Overview

Starting ChemDraw

Working With Documents

Printing

Quitting/Exiting

ChemDraw's Graphical Interface

Customizing your environment


Chapter 2, Getting Started Tutorials

Overview

Tutorial 1: Reaction Schemes

Tutorial 2: Drawing an Intermediate

Tutorial 3: Using Rings

Tutorial 4: Fischer Projections

Tutorial 5: Perspective Drawings

Tutorial 6: Newman Projections


Chapter 3, Drawing Chemical Structures

Overview

Single Bonds

Multiple Bonds

Ring Tools

Acyclic Chains

Drawing Settings for Bonds

Editing Bonds


Chapter 4, Captions and Atom Labels

Overview

Captions

Atom Labels

Entering non-Roman Text

Text Format

Tables


Chapter 5, Drawing Orbitals and Chemical Symbols

Overview

The Orbital Tool

The Chemical Symbol Tool


Chapter 6, Drawing Arrows, Arcs and Other Shapes

Overview

The Arrow Tool

The Drawing Elements Tool

The Arc Tool

The Pen tool


Chapter 7, Working with Selections

Overview

Using the Selection Tool

Moving Objects

Duplicating Objects

Rotating Objects

Reflecting Objects Through Planes

Resizing Objects

Joining Objects

Grouping


Chapter 8, Advanced Drawing Techniques

Overview

Using HotKeys to Label Atoms

Nicknames

Multi-center Bonds

Creating a Multi-Center Bond

Multi-attached labels

Expanding Labels

Variable Attachment Positions

Structure Clean Up

Checking Chemistry

Analyze Structure

Working With Color


Chapter 9, Drawing Query Structures

What Are Query Structures?

Atom Properties

Bond Properties

Generic Nicknames

Element Lists

Element Not-Lists

Alternative Groups

Multiple Attachment Points

Anonymous Alternative Groups

Export Compatibility


Chapter 10, Drawing With Templates

Overview

The Template Tool

Drawing with Templates

Creating Templates and Template Documents


 Chapter 11, Reactions

Overview

Automatic Mapping

Manual Mapping

Clear Mapping

Exporting Reaction Map


Chapter 12, Working with Page Layout

Overview

Controlling the Drawing Area

Arranging Objects


Chapter 13, Sharing Information

Overview

Working Between ChemDraw Documents

Embedding Objects

Importing and Exporting

Exporting and Importing using File Formats


Appendix A, The Chemistry of ChemDraw

Overview

Is all of this really necessary?

Chemistry In ChemDraw


Appendix B, Specifying Paths

Overview

Windows:

Macintosh:


Appendix C, Technical Support

Overview

Serial Numbers

Troubleshooting


Appendix D, Document Settings

Overview


Appendix E, Apple Events (Macintosh)

Overview


Appendix F, Chemistry File Formats

Overview

Example of Other File Formats


New in 4.5

·	In ChemDraw Pro, the Reaction Atom-Atom Mapping tool in the tools palette and the Map Reaction Atoms and Clear Reaction Atoms commands in the Structure menu have been added. These features give you the ability to create reaction maps for query searching reaction databases.

·	In ChemDraw Ultra, estimate Chemical Properties  such as LogP

·	In ChemDraw Ultra, calculate proton and C13 NMR chemical shifts

·	The Selection tool has been changed to be two separate tools, the Lasso tool functions the same as the old style Selection tool, the Marquee uses the Marquee mode of selection as the default. The mode of either tool can be toggled to that of the other by using the Ctrl key (Windows) or the Option key (Macintosh).

·	Using either the Lasso or Marquee tool, selecting has been enhanced to allow single atom selection.

·	A new menu, the Structure menu, has been added to contain chemistry specific commands. This menu contains many of the items previously in the Object menu as well as the new Map Reaction Atoms and Clear Reaction Atoms commands.

·	The Alternative Groups  tool now has a new icon

·	The Attachment Point tool now has a new icon

·	In the Windows 95 version, the Open, Save and Print dialogs have been updated to the Window 95 style.

·	In the Windows version, a status bar has been added to the application window.

·	In the Windows version, a tool bar has been added to the application window.

·	In the Windows version, tool tips are displayed when you point to items in menus, the tools palette or the tool bar.

·	You can now save ChemDraw documents in TIFF or PNG  file format.


Overview

ChemDraw is designed to aid professional scientists and scientific authors in the task of communicating chemical structures. ChemDraw employs a straightforward graphical interface. Because ChemDraw is designed specifically for communicating chemical structures, ChemDraw automatically employs conventions that are intuitive to people who routinely work with chemical structures.

Quite a bit of thought and experimentation has been put into making ChemDraw as easy to use as possible while providing superior drawing quality. We hope you find ChemDraw a useful tool.


About this User's Guide
About this Help File

This manual covers CS ChemDraw for Windows and Macintosh platforms. The pictures in the manual have been taken from both platforms, and therefore may differ from what you see on your screen.

More:

Documentation for UNIX users


Documentation for UNIX users

Documentation for the UNIX version of CS ChemDraw is provided in an on-line manual (in Adobe Acrobat PDF format). This file is located on the CD that came with your software.


Organization of this User's Guide
Organization of this help file

The majority of this help file is designed in a task oriented fashion. For example, to learn how to draw a bond, refer to Chapter 3, Drawing Chemical Structures. To learn how to position objects in the document window, refer to Chapter 12, Working with Page Layout. For basic operations, refer to your operating system documentation.


Conventions

The following notations are used throughout this help file:

 The Pro symbol indicates that a feature is available in CS ChemDraw Pro only.

The Ultra symbol indicates that a feature is available in CS ChemDraw Ultra only.

·	Instructions are always preceded by a bullet "·" and shown in bold type.

Notes are used throughout this help file to highlight information that may be out of context to the current discussion.

NOTE:

The following terminology is used throughout this help file:

·	"Point" refers to moving the mouse until the mouse pointer is over the item you want.

·	"Click" refers to quickly pressing then releasing the left mouse button.

·	"Double-click" refers to clicking the left mouse twice in rapid succession.

·	"Drag" refers to the following complete action: holding down the left mouse button, moving the mouse, and releasing the mouse button.

·	"Select" means to highlight an object or choose an option. Selecting something does not initiate an action. However, it marks the item upon which you want to act or provide information. Deselect is the opposite of select.

·	"Choose" means to select a command from a menu or submenu, or to click a Toolbar button, or to click a button in a dialog box that completes or cancels a command. Choosing an item performs a command.

·	"Key+click" means to hold the specified Key and click the mouse button. For example, Shift+click means hold down the Shift key and click the mouse button.

·	"Key+drag" means to hold down the specified key and drag a selection. For example, Shift+drag means to hold down the Shift key and drag the pointer.


Getting Additional Help

A Quick Reference card for ChemDraw is found at the back of your user's manual. This card provides summaries to the commands and features for this application. The Quick Reference cards should be used as you run through the tutorials in Chapter 2, Getting Started Tutorials, since many of the instructions require the knowledge of elements of the interface.

In the Macintosh version, you can use Balloon help by choosing Show Balloons from the Help menu. Once started, you can point to objects of the ChemDraw interface and read short paragraphs about the object within the balloon that appears.

Macintosh users can also use Apple Guide (tm). We have provided several simple tutorials that guide you through basic techniques for drawing structures.

In the Windows version, you can use tool tips by pointing at an item in the Tool bar, Tool palette or menu item to display a short description of the item in a pop-up message.


Installation/System Requirements

To install ChemDraw, refer to the "Read Me First" document that came with your software. In addition, late breaking news concerning installation can be found in the Read Me file (Macintosh) or Readme.txt (Windows) on your installation disk or CD-ROM.

Windows System Requirements:

ChemDraw runs on most IBM compatible computers having a minimum of a 486 processor. The operating system must be either Windows NT (version 3.5 or later), Windows (version 3.1 or later) or Windows 95.

To run under Windows 3.1 requires a minimum of 8 MB of RAM. In addition, you must install the WIN32s DLLs that come with the installation disks and virtual memory must be turned on.

To run under Windows 95 requires a minimum of 8 MB of RAM and virtual memory turned on.

To run under Windows NT 3.5 or later requires a minimum of 12 MB of RAM.

You will need a hard drive with at least 10 MB of available disk space.

Macintosh System Requirements:

ChemDraw can run on any 68020 or later Macintosh or Macintosh-compatible computer that supports MacOS version 7.0 or later and has a minimum of 8 MB of RAM.

You will need a hard drive with at least 5 MB of available disk space.


Chapter 1, ChemDraw Basics - Overview
Overview

This chapter discusses the basic information required to begin using ChemDraw. You will learn how to start a session, create, open and save documents, identify the parts of the ChemDraw application and customize certain aspects of the user environment.


Starting ChemDraw

You can start the ChemDraw application in several ways:

·	(Macintosh) From your desktop you can double-click the ChemDraw application icon, or select the icon with a single click and choose Open from the File menu.

·	(Windows) From the Program Manager, File Manager (Windows 3.1 or NT) or Explorer (Windows 95 and Window NT 4.0) you can double-click the ChemDraw application.

In all cases, ChemDraw is launched and a new document is created.


Working with Documents

This section deals with issues concerning the creating, opening and saving of ChemDraw documents.

More:

Creating Documents

Opening Documents

Saving Documents

Discarding Recent Changes to a Structure

Viewing the Location of a Document (Macintosh only)

Closing Documents

Accessing Documents Quickly


Creating Documents

To create a new document:

·	From the File menu, choose New.

NOTE: The New Document command in the File menu uses a Style Sheet(Windows) or Stationery Pad (Macintosh) with settings that are commonly used for the majority of documents.

To create a new document using a different Style Sheet(Windows)

·	From the File menu, choose Open Special.

·	Choose a Style sheet from the list.

A new document is created that has the settings (and objects) stored in the Style Sheet.

To create a new document using a Stationery Pad (Macintosh)

·	From the Window menu, choose a stationery document.

A new document is created that has the settings (and objects) stored in the Stationery Pad.

More:

More about Style Sheets/Stationery Pads


More about Style Sheets/Stationery Pads

ChemDraw comes with a number of pre-defined Style Sheets/Stationery Pads which are located in the cd_items directory (Windows) or the ChemDraw Folder (Macintosh). For example, the ACS-1996 document is pre-configured to create documents that are set with the bond lengths, bond width, spacing and fonts commonly used in the 2-column format within the Journal of the American Chemical Society. A list of the settings stored in these documents is provided in Appendix D, Document Settings.


Opening Documents

To open a ChemDraw document.

·	From the File menu, choose Open

The Open dialog box appears.

·	Select the location where the file is stored.

·	Select the name of the file.

·	Click the Open button (Macintosh) or OK button (Windows).

To open a file in a different file format choose the file format of the file from the pop-up menu at the bottom of the dialog box before clicking the Open/OK button. See "Exporting and Importing using File Formats" in Chapter 13, Sharing Information, for more information.

More:

Switching Between Open Documents


Switching Between Open Documents

Each time you open a document, a document window appears. If you have opened more than one document, the document windows are stacked. The frontmost document is the active window where you can actually do work. All open documents are listed in the Window menu.

There are several ways to make another open document the active window:

·	From the Window menu, choose the document.

·	Or, click any exposed area of the window you want to be the active window.

·	Press Ctrl+Tab to switch between the currently open document windows (Windows only)


Saving Documents

To save a ChemDraw document:

·	From the File menu, choose Save.

The Save dialog box will appear.

Depending on the platform you are working under, the dialog box will differ. In the Macintosh version, you will find and Options button. This button is dimmed unless you choose the TIFF file format, in which case you can choose from various color, resolution and compression optiosn for the TIFF file.

NOTE: In the Macintosh version, there is also a Go To ChemDraw Folder button. For further details, see "The ChemDraw Folder" later in this chapter. NOTE: ChemDraw (*.cdx) is the native format that ChemDraw recognizes as its own. As such, all information about the structure will be accurately stored. Other file formats may lose information because of those formats internal structure. For instance, under Windows, saving a file as EPS will remove the chemical significance of the connection between atoms and bonds, and store only a picture of the structure. EPS files in Windows do not store a preview.

·	Type a name for the file in the box named "File Name" (Windows) or "Save As" (Macintosh).

The Macintosh, Windows 95 and Windows NT operating systems allow you to type up to 32 characters for a file's name including spaces (for example, "my first structure in ChemDraw") However, if you are using the Windows 3.1 operating system you must type a name using the 8.3 convention (for example, "myfile.cdx").

·	Choose a directory (folder) in which to store the file.

·	Click the Save button (Macintosh) or OK button (Windows) to create the file.

When you save a document in the native ChemDraw file format the name of the window changes to the name that you typed indicating that a file has been created in the location that you specified.

Even though you have now created a physical file for storing information, you still must save your work frequently. Any new information that you add to the window is stored in your computer's memory (RAM) until you again save it.

To save a window that has previously been saved:

·	From the File menu, choose Save.

The contents of the file will be updated with the information currently in the window. The dialog will not be displayed.

More:

Saving a Document with a Different Name or Location

Saving a Document in a Different File Format


Saving a Document with a Different Name or Location

You can use the Save As command to save a copy of your document under a different name, save a copy to a different location, or save a copy using a different file format. Saving a copy under a different name or location is useful for keeping earlier revisions of your document. Saving a file as a different type is useful for creating Style Sheets/Stationery Pads and for exporting information to other applications.

To save a copy of a ChemDraw document under a different name or in a different location:

·	From the File menu, choose Save As.

·	Type a new name of the file in the Save dialog box and/or choose a new location in which to save.

·	Click the OK button (Windows) or Save button (Macintosh).


Saving a Document in a Different File Format

To save a ChemDraw document in another file format:

•	From the File menu, choose Save As.

The Save As dialog box appears.

•	Select a file format from the File Format pop-up menu or from the Save File as Type drop-down list box.

NOTE: In the Macintosh version, the Options button becomes undimmed when the TIFF file format is selected. Clicking this button opens an option dialog for setting color resolution and compression options. See Chapter 13, Sharing Information SharingInformationfor more information about TIFF options.

•	Type a name for the document in the File Name box.

•	Select a directory/folder and disk in which to save the document.

•	Click the OK button (Windows) or Save button (Macintosh)

Be aware that if you type a name that already exists for a document that is in the same directory, it will replace the existing version of the document. It is best to use a different name so you do not replace the original ChemDraw document. For a discussion of other file formats, see Chapter 13, Sharing Information.

The original document in the ChemDraw format remains in the active window. The file in the other format is saved with the name and in the location you specified. You should consider saving files in other formats only when they are at a stage where they are complete, not in progress.


Discarding Recent Changes to a Structure

To retrieve the last saved version of a file:

·	From the File menu, choose Revert.

All changes made to the file since it was saved last are discarded and the previous version of the file appears.

NOTE: You can use the Undo command in the Edit menu to remove each individual action since the last save, see "Undoing Actions" for more information.

NOTE: In all ASCII text file formats, the front to back ordering of atoms and bonds are saved in the file, rather than the order in which they were drawn.


Viewing the Location of a Document (Macintosh only)

To view the folder(s) where the document in the frontmost window is located:

·	Point to the name of the document in the title bar.

·	Hold the Command key down and press the mouse button.

A pop-up menu appears describing the location of the document. The second item in the pop-up menu is the name of the folder (or the disk if there are no folders) that contains the document. The last item in the pop-up menu is the name of the disk that contains the document.

Figure 1-3 Location of a ChemDraw Document

To switch to a folder in the listing:

·	Select a folder or disk from the pop-up menu.

The folder you chose becomes the active window. The ChemDraw document is in the background.

To return to your ChemDraw document.

·	Click in the window containing your document or choose ChemDraw from the Application Icon menu to make it the active application.

The ChemDraw document is moved into the active window.


Closing Documents

When you are finished with a document you can close the document window, and file it away.

To close the active window:

•	From the File menu, choose Close.

The document in the active window is closed. If you have made any changes to this document since last opening or saving, you will be asked if you want to save the document before closing the window.


Accessing Documents Quickly

You can quickly access ChemDraw documents using the ChemDraw Folder (Macintosh) and the cd_items directory (Windows).

More:

The ChemDraw Folder (Macintosh)

The Windows Menu (Macintosh Only)

The cd_items directory (Windows only)

Changing the Default Directory (Windows only)

The Window Menu (Windows only)


The ChemDraw Folder (Macintosh)

The ChemDraw Folder is a special folder that is normally located in the same folder as your ChemDraw application (however, it can also be located in the Preferences Folder within your System Folder).

ChemDraw documents contained within the ChemDraw Folder are automatically added to the Windows menu. This is useful for accessing documents that you commonly use, such as Stationery Pads (and Template documents and Template Stationery Pads in ChemDraw Pro).

Other files contained within the ChemDraw Folder, include the ChemDraw Preferences file, scripts, ChemDraw HotKeys file, the ChemDraw Nicknames file, the isotopes file which contains the isotopes and elements used by ChemDraw and the generic nicknames file. However, these files do not appear in the Windows menu (scripts appear in the Scripts menu).

NOTE: You can place aliases of template files or Stationery Pads in your ChemDraw Folder. The originals can come from another folder on your computer or another computer that is on your network. You can then access the alias from the Windows menu.


The Windows Menu (Macintosh Only)

The Windows menu contains two groups of documents: Those currently open and those located in the ChemDraw Folder. Choosing any of the documents in the Windows menu performs the same function as opening the same document by one of the standard methods discussed earlier in this chapter. For instance, choosing an open document will make that document the active window. Choosing a Stationery Pad will open an untitled document based on that Stationery Pad, and so on.

Document types are listed in segments within the Windows menu. Documents within each segment are listed alphabetically. The first segment contains documents that are currently open, both ChemDraw documents and Template documents. The open document that is the active window has a checkmark next to it. The second segment lists all Stationery Pads contained within the ChemDraw Folder, both ChemDraw stationery and Template Stationery Pads. The third segment lists any other ChemDraw documents or Template documents contained within the ChemDraw Folder. The icons for each of the document types are slightly different so that you can distinguish among them.

NOTE: The Template documents and Template Stationery Pads only appear in ChemDraw Pro.


The cd_items directory (Windows only)

The cd_items directory is a special directory, usually located in the same directory as the ChemDraw application (however, it can also be located within the system directory within the Windows directory - see Appendix B, Specifying Paths SpecifyingPathsto alter the path to the cd_items folder.).

ChemDraw documents located within this directory are accessible from the Open Special submenu in the File menu. This is useful for accessing documents that you commonly used, such as Style Sheets (and Template documents and Template Style Sheets in ChemDraw Pro).

Other files contained within the cd_items directory include the ChemDraw Preferences file, ChemDraw HotKeys file (hotkeys.txt), ChemDraw Nicknames file (nickname.dat), the Isotopes table (isotopes.txt) which contains the isotopes and elements used by ChemDraw and the generic nicknames file (generics.txt). However, these files do not appear in the Open Special submenu


Changing the Defualt Directory (Windows Only)
Changing the Default Directory (Windows Only)

When you choose to open or save a file, ChemDraw automatically displays in the Open or Save dialog the same directory that contains the ChemDraw application. You can change the default directory by modifying the icon you double-click to launch ChemDraw.

To change the default directory in Windows 3.1:

•	Select the ChemDraw application icon in the Program Manager.

•	Press ALT+ENTER.

•	Enter the desired default directory in the Working Directory field.

•	Press OK.

To change the default directory in Windows 95, Windows NT 4.0, and later versions of Windows:

•	Select the ChemDraw application icon in the Windows Explorer.

•	From the File menu, choose Create Shortcut

•	Select the Shortcut to ChemDraw icon

•	Press ALT+ENTER.

•	Choose the Shortcut tab

•	Enter the desired default directory in the Start In field.

•	Press OK.

You can then use this modified icon or shortcut whenever you want to launch ChemDraw.


The Window Menu (Windows only)

The Window menu lists all open ChemDraw documents (and open Template documents, in ChemDraw Pro). In addition, the Window menu contains other standard Windows commands for organizing your document windows and icons within the Application window, such as tiling and cascading. Choosing a document from the Window menu performs the same function as opening the same document by one of the methods discussed earlier in this chapter. The document you choose becomes the active window.


Printing

ChemDraw uses the standard system commands to print ChemDraw documents. The options that you have available to you will depend on the printer that you are using. You should refer to your printer's documentation for these specifics. In general however, to print a ChemDraw document:

·	From the File menu, choose Page Setup (Macintosh) or Print Setup (Windows).

Make all appropriate selections for the printer you are using and click the OK button.

·	From the File menu, choose Print.

·	Make your selections in the Print dialog box and choose the Print button.

Alternatively, to print a document from the File Manager or from the Finder:

·	Select the document you want to print.

·	From the File menu, choose Print.

The ChemDraw application is opened and the Print dialog box appears.

·	Make your selections in the Print dialog box and choose the Print button.

Preferences Guide

Print Background Color

You can control whether the Background Color contained in your ChemDraw document is printed.

To change whether the Background Color is printed:

·	From the File menu, choose Preferences.

·	Click the Print Background Color check box.

·	Click the OK button.

This change affects all documents.

NOTE: You can specify whether the Background Color contained in your ChemDraw document is printed by selecting or deselecting the Print Background Color option in the Preferences dialog box.

(Macintosh) If you are transferring information to another application from which you will print ChemDraw pictures, you will need to consider including PostScript commands and the ChemDraw LaserPrep File with the pictures. To learn about the special situation to consider, refer to "Transferring PostScript" in Chapter 13, Sharing Information.

More:

Print Quality


Print Quality

(Macintosh) When you print a document, ChemDraw creates both a QuickDraw representation and a PostScript representation of the document's contents.

QuickDraw is the graphical format that is supported by the Macintosh Operating System. Every printer to which you can print from a Macintosh can convert QuickDraw representations into printed output. However, because QuickDraw is supported by all printers, it does not offer good support for features (like high-resolution printing) that are available only on some printers.

Preferences Guide (Macintosh)

Optimize Pictures for High-Resolution Non-PostScript Printing

Several years ago, Apple enhanced the way the clipboard behaves to better support high-resolution printers. This method uses a High Resolution Clipboard and while it still is QuickDraw based, it can offer much better output quality.

Although ChemDraw supports the use of this High-Resolution Clipboard, it also needs to be supported in the program into which you are pasting your pictures. Besides ChemDraw, some programs that support the High Resolution Clipboard include PageMaker, MacDraw, KaleidaGraph, and IGOR Pro. Microsoft Word (through version 6.0, at least) is a prime example of a program that does not support the High-Resolution Clipboard.

If you are unsure if the application uses a High Resolution Clipboard, try transferring pictures with this checkbox selected and deselected and see which picture prints with higher quality. In addition, if you are printing to a non-PostScript printer, deselect the checkboxes labeled "Include ChemDraw LaserPrep" and "Include PostScript" to reduce the size of each picture by 11K to 12K.

To use the High Resolution Clipboard:

·	From the File menu, choose Preferences.

·	Click the Optimize Pictures for High-Resolution Non-PostScript Printing checkbox.

·	Click the OK button.

If you are printing to a PostScript printer, you should turn on the Include PostScript option instead. PostScript will always offer the highest-quality output. For more information, see "Transferring PostScript" in Chapter 13, Sharing Information.

This change affects all documents.

The PostScript representation is used by printers that use the PostScript page definition language, such as the Apple LaserWriter NT, and most brands of typesetters. The PostScript representation describes objects precisely by using mathematical shapes that can be precisely imaged at whatever resolution is used by your printer. The PostScript representation created by ChemDraw is composed of two parts, the PostScript commands and the ChemDraw Laser Prep. The ChemDraw Laser Prep contains specific instructions that enable the printer to interpret the PostScript commands contained in a ChemDraw document.

Preferences Guide (Macintosh)

Include PostScript

If you are transferring ChemDraw pictures to another document that will be printed on a PostScript printer:

·	From the File menu, choose Preferences.

·	Select the Include PostScript checkbox, then click the OK button.

When Include PostScript is not checked, no PostScript commands are generated. This will usually result in lower quality printing, particularly of drawings cut and pasted into other applications. However, since the representation used for printing when Include PostScript is not selected is the same as that used for drawing to the screen, better correspondence between the screen and printed output might be observed in some cases.

Include ChemDraw LaserPrep

Select this checkbox for maximum flexibility when printing to PostScript printers. If you do not select this checkbox, you will need to choose the Initialize LaserWriter command from within ChemDraw before you print. If you create pictures with this off and then give them to a colleague, they will be unable to print them to PostScript printers unless they also own a copy of ChemDraw and can choose the Initialize LaserWriter command themselves.

For more information, see "Transferring PostScript" in Chapter 13, Sharing Information.


Quitting/Exiting

Quitting an application frees up the memory the application uses so that other applications can have more memory available to them. To close the ChemDraw application:

·	From the File menu, choose Quit ChemDraw (Macintosh) or Exit ChemDraw (Windows).

If you have document windows open that have not been saved, you are first asked if you want to save them before you close the application.


ChemDraw's Graphical Interface

One of the best things about ChemDraw is the simplicity of its interface (the part of the application that you interact with to perform tasks). The interface consists of a document window, menus, tool bar (Windows only), commands, a tools palette and a status bar/message area. These items are described below.

More:

Document Window

The Tools Palette

Menus and Commands

Using Dialog Boxes

Undoing Actions

Redoing Actions


Document Window

The central part of the document window contains the work space where you will draw your structures. The Tools palette contains icons for tools that change the way the pointer (cursor) behaves.

The basic components of a ChemDraw document window are shown below.

Figure 1-6 The ChemDraw document window

Table 1-1 Parts of the document window

Screen Element	Use
Drawing area	The area within a document window where you can draw.
Menu bar	Contains all the commands specific to the ChemDraw application for manipulating documents and their contents.
Message area	Contains short information messages that appear as you draw, such as the length and angle of bonds or the magnification of the window. In the Windows version the message are is a Status Bar that also display tool tips and magnification.
Scroll arrows	Scrolls a document window in small increments in the direction of the arrow
Scroll bars	Scrolls a document window in large increments.
Scroll boxes	Scrolls a document window in the direction that you drag the box.
Title bar	Contains the name of the application or document as a Window Title. Also, the Title bar can be dragged to move a window.  (Macintosh) Holding down the Command key and pressing and holding down the mouse button over the title displays the location of the ChemDraw document.
Tool bar (Windows only)	Contains icons for commonly used commands which you can click to invoke the command as an alternative to choosing the corresponding command in a menu.


The Tools Palette

The Tools Palette (Figure 1-7) contains the tools that you can use to draw in a document window. Tools are selected by clicking a tool icon. One tool in the Tools palette is always selected. Tools with a small triangle in the lower right corner contain a palette of choices for the tool. Holding down the mouse button over this type of tool displays the palette. A description of each tool is found in Table 1-2.

Figure 1-7 Tools Palette

Table 1-2 Tools in the Tools window

Tool Name	Use
Bond Tools	Used for drawing single, double and triple bonds of various types.
Acyclic Chain Tool	Used for quickly drawing chains of any length.
Arc Tool	Used for drawing arcs. Arcs of different degrees can be selected from the Arc Tool's palette.
Alternative Group Tool	In ChemDraw Pro, this tool is used to create alternative group definitions (R, G, etc) that represent a set of substituents, any one of which will match the query.
Reaction Atom-Atom Map Tool	In ChemDraw Pro, this tool allows you to create correspondences between atoms in different structures for use in creating queries for searching a reaction database.
Attachment Point Tool	In ChemDraw Pro, this tool is used to specify attachment point in an alternative group definition.
Arrow Tool	Used to draw arrows. Arrows of different types can be selected from the Arrow Tools palette.
Chemical Symbols Tool	Used to draw chemically significant symbols such as charges, radicals and lone pairs.
Drawing Elements Tool	Used to draw objects common to reaction schemes, such as brackets and lines. Drawing Elements of different types can be selected from the Drawing Element Tools palette.
Eraser Tool	Used to delete objects.
Orbital Tool	Used for drawing orbitals. Orbitals of different types can be selected from the Orbital Tools palette.
Ring Tools	Used for quickly drawing common structural components.
Pen Tool	Used to draw freehand shapes such as custom arrows and orbitals.
Lasso Tool	Used to select objects by dragging around them. Objects that are selected can be further manipulated using menu commands.
Marquee Tool	Used to select objects by dragging diagonally across them. Objects that are selected can be further manipulated using menu commands.
Selection Tool	Used to select objects. Objects that are selected can be further manipulated using menu commands.
Template Tool	Used for drawing structures using templates stored in template documents. Templates can be selected from the Template Tools palette.
Text Tool	Used to create atom labels and captions.


Menus and Commands

The menus in the menu bar contain the commands that you use to perform tasks on a document.

There are several ways to access commands within menus. The three possibilities available in ChemDraw are:

1. Mouse: You can display the commands in a menu by pointing to a menu name, hold down the mouse button and drag to the command you want to choose. On Windows, you may alternatively point to the menu name, click it to select and open the menu, then point to the command you want to choose and click the mouse button.

2. Alt, letter, letter: (Windows only) Press the Alt key and then press the underlined letter in the menu name you want to open, release this key and press the underlined letter in the command you want to choose. For example, Alt, F, X opens the File menu and chooses the Exit ChemDraw command. If you open a menu and decide not to choose a command you can press the Alt or ESC key to close the menu, or use an Arrow key to open another menu.

3. Command shortcuts: Many commands have keyboard equivalents that you can memorize and use to execute a command directly without first opening the menu. For example on Macintosh, [image] is equivalent to choosing New from the File menu and under Windows, Alt+F4 is equivalent to opening the File menu and choosing Exit ChemDraw. The available command key equivalents are listed next to the menu commands.

The appearance of the commands in a menu may change. The different appearances of commands are described in Table 1-3.

Table 1-3 Appearance of commands

Menu Convention	Meaning
Checkmark next to a command	The command is currently turned on, or in effect. Usually, selecting the command again removes the check mark.
Partial Selection marksnext to several commands	Indicates that each selected command applies to part of the current selection (these appear as hyphens under Macintosh)
Dimmed command(grayed out command)	The command is not available for the current selection, or for the state of the active document . or is not available in this version..
Ellipsis (...)after a command	A dialog box appears which requires user input before the command is executed.
Key combination next to a command	You can use the command key combination to execute the command rather than choosing it from the menu.
Trianglenext to a command	Indicates that if you press and hold down the mouse button on the name of the command, a submenu with further options appears.


Using Dialog Boxes

Dialog boxes appear when additional information is required to complete commands.

Within a dialog box, there are several ways to navigate:

1. Mouse: You can click an option to select it, or click a command button to complete or cancel a command.

2. Keyboard: To move within the dialog box you can press the Tab key to go to the next button or option group, or you can press Shift+Tab to move back to the last button or option group. Option groups and their navigation techniques are discussed in the table that follows.

The different options available are described in Table 1-4.

Table 1-4 Options in dialog boxes

Option Type	Use
Check Boxes	Check boxes are selected when an "x" appears in the box. You can select as many check boxes as you need. Check boxes without an "x" are deselected.
Drop-down List Boxes or Pop-up Menus	Drop-down list boxes (Windows) or pop-up menus (Macintosh) provide a list of possible options from which you can choose, much like the menus in the menu bar.
Command Buttons	Command buttons generally are used to execute the information, or to cancel any changes made. Common command buttons are the OK and Cancel buttons.  In most dialog boxes, a default button exists for executing the command, for example the OK button. The default button has a bolder outline and can be chosen by pressing the Return key.
Option Button or Radio Button	The items in a group of option buttons (Windows) or Radio buttons (Macintosh) are mutually exclusive. You can only select one option button in a group.
Spin Button or Control Arrows	Spin buttons (Windows) or Control Arrows (Macintosh) provide a range of values from which you can select. To select a value, click the up or down arrow on the spin button, or type a value in the text box next to the spin button.
Text Box	A text box is used to enter textual information, such as a file name. To enter information within a text box, simply point to the box and click to select the text in the box. Next, type the necessary information.


Undoing Actions

ChemDraw keeps track of the actions you perform. You can reverse actions one at a time by choosing the Undo command. The number of actions that can be undone or redone is limited only by the amount of memory (i.e., RAM and virtual memory) available for use by ChemDraw. When you save your document the Undo queue is reset and starts over.

To undo the last action performed:

·	From the Edit menu, choose Undo.

The last action performed is reversed. The Redo command changes to reflect the undone action. The Undo command changes to reflect the next action you can undo.

For example, if you draw cyclohexane, create an atom label text box, type a label, and select and rotate the structure, you will be able to remove the actions as follows:

1. Remove the rotation.

2. Remove atom label.

3. Remove the ring.

At each step, the Undo command is appended with the action being removed.


Redoing Actions

When you undo an action, the Redo command becomes active. You can reverse the effect of the Undo command by choosing the Redo command. The Redo command is appended with the action being redone.

To redo the last action performed:

·	From the Edit menu, choose Redo.

The last action undone is reinstated. The Undo command changes to reflect the next action you can undo. The Redo command changes to reflect the next action that can be redone.


Customizing your environment

In ChemDraw there are many ways to customize your work. Preferences allow you to change the default behavior of certain options that will be in force for every open document. Document Settings allow you to change the default behavior of options that will affect only the frontmost document. In addition, you can customize your menus by adding commands that perform tasks using other applications by adding Scripts (Macintosh) or through menu extension DLLs (Windows).

More:

Preferences

Document Settings

Saving Customized Settings

Applying Settings From Other Documents

Scripts (Macintosh Only)

Menu Extension DLLs (Windows Only)


Preferences

Preferences affect the way the ChemDraw application works, regardless of the document with which you are working. Preferences affect things like the units of measurement that you use. Preferences are saved in the ChemDraw Preferences file located in the System folder (Macintosh) or the chemdraw.ini file which is located with the Windows directory (Windows).

As you become familiar with the application, you can change the preferences to suit your needs. Preferences are described as the topic to which they apply is discussed.

Table 1-5 Preferences options

select this preference.	if you want to...
Units	change the units used in the Drawing Settings dialog box, the Rulers and the Crosshair. Available units include inches, centimeters and points.
Tolerance	change the size of the highlight box that appears when you point at any object in the document window. The tolerance affects how close the cursor needs to be for selecting or joining.
Include Footer	print a footer containing the document name, date and time of the last revision. The footer appears in the lower left corner of a printed document.
Include PostScript (Macintosh only)	transfer ChemDraw pictures to other applications that will eventually print to a PostScript printer. ChemDraw pictures can be transferred through any of the following: the Clipboard, or Publish. If you are printing to a non-PostScript printer, you can leave this checkbox unchecked.
Include ChemDraw LaserPrep In Pictures (Macintosh only)	print to a printer that cannot be initialized using ChemDraw (for instance, a service bureau). You should also check the Include PostScript option if you select this option. If you are printing to a non-PostScript printer, there is no need to have this checkbox checked. NOTE: This PostScript information will add an extra 11 to 12K per picture to the destination document; however it insures that the document containing the ChemDraw pictures can be printed. This affects Clipboard, Publish,, and EPS files.
Show 35mm Slide Boundary Guides	display boundary guides to help you keep your picture in the appropriate ratio for the 35 mm slide format.  Boundary lines appear at 7 inches and 10.5 inches. The page size must be at least 7 x 10.5 inches for the boundary guides to appear. The boundary guides are not printed.  NOTE: This option to print slides is merely an assistant to keeping your structures within the bounds of the standard 35 mm slide dimensions.
Require Ctrl-Enter to Create New Line (Windows) or Require Option + Return to Create New Line (Macintosh)	use the Enter key (or Return key for Macintosh users) to close text boxes. When this option is selected, you will need to hold down the Ctrl key and press the Enter key (or the Option and Return key for Macintosh users) to add a new line.
Optimize Pictures for High Resolution Non-PostScript Printing (Macintosh only)	transfer ChemDraw pictures to another application that uses a High Resolution Clipboard and will be printing the document to a non-PostScript (QuickDraw) printer. If you are unsure if the application uses a High Resolution Clipboard, try transferring pictures with this checkbox selected and deselected and see which picture prints with higher quality.
Use Bitmap Fonts When Available (Macintosh only)	display text on screen using Bitmap fonts rather than TrueType fonts. The text will appear more quickly, and for some fonts, such as Helvetica, the on-screen display is more readable. If this option is deselected, text may be less readable on the screen, but will more accurately represent the size and position of the printed text.
Automatic Atom Labels	have ChemDraw use Automatic justification for new labels. Automatic labels are repositioned and Hydrogens are added or removed as bonds are added or moved. With this option deselected, new labels are Flush Left, Centered, Flush Right, or Stacked Above, depending on the positions of the bonds to the atom.
Print Background Color	print the background color. With this option deselected, the background will always print as white.
Check Structure When Copying to Clipboard or Exporting	invoke the Check Structure command when a structure is copied to the Clipboard or saved. This provides a safety check for structures that you will be importing into other applications, such as ChemFinder.
Show Attachment Rank Indicators	in ChemDraw Pro, used to show visual indication of the attachment point ordering in alternative groups.
Always Display and Print Reaction Mapping	in ChemDraw Pro, used to show visual indication of atom mapping created using the Reaction Atom-Atom Map tool
Automatic Atom Mapping	in ChemDraw Pro, when selected, will automatically complete atom mapping after an atom-atom map is manually defined using the Reaction Atom-Atom Map tool.


Document Settings

Document settings are user definable settings that are applied to the current document. Document settings include Drawing Settings, Caption Text Settings, Label Text Settings, Print/Page Setup, and the Color Palette. Drawing Settings affect drawing related options such as the fixed length used to draw bonds. Text Settings affect text related options like the font used for atom labels and captions. The Color Palette affects the colors available to Colorize objects. The Print/Page Setup affects options like the page size used.

As you become familiar with ChemDraw you can change these settings to fit your needs. You can also save different sets of document settings in Style Sheets/Stationery Pads to be used for special instances, such as journal articles, textbook chapters, slide presentations and so on. See “Saving Customized Settings, earlier in the chapter, for more information.

More:

Drawing Settings

Text Settings

Color Palette


Drawing Settings

Drawing Settings are document settings that affect how bonds are drawn. Changes made in the Drawing Settings dialog box (Figure 1-9) take effect for all bonds already drawn as well as those that are drawn later with the exception of the fixed length setting, which only applies to newly-drawn bonds. Changes made affect the active document window only. Drawing settings can be saved in Style Sheets/Stationery Pads

A summary of each of the options is described in table 1-6 below:

Table 1-6 Drawing Settings options

Adjust this setting...	If you want to...
Chain Angle	change the angle (from 1 to 179 degrees) between bonds created by the Acyclic chain tool or modified by the Clean Up Structure command For more information see the "Acyclic Chain Tool" in Chapter 3, Drawing Chemical Structures DrawingChemicalStructuresand "Structure Clean Up" in Chapter 8, Advanced Drawing Techniques .
Bond Spacing	change the distance between the lines in double or triple bonds. The distance is set as some percentage of the total length of the bond (between 1 and 100). This allows for proportional spacing to be used if different bond lengths are used in the drawing.
Fixed Length	constrain the length of the bonds drawn to the length you specify whenever the command Fixed Lengths in the Tools menu is selected (a checkmark is next to it). This will also adjust the preferred bond length for structures modified by the Clean Up Structure command.
Bold Width	change the width of the line used when bold and wedge bonds are drawn.
Line Width	change the width of all bonds, lines and arrowheads in the drawing.  .
Margin Width	change the amount of space surrounding all atom labels that will erase portions of the bonds to which they are attached. The margin width also determines the amount of white space surrounding the front bonds in a bond crossing.
Hash Spacing	change the spacing between the hashed lines used when wedged hashed bonds, hashed bonds, dashed bonds, dashed arrows or dashed curves are drawn.


Text Settings

Text Settings (Macintosh) or Caption Text Settings and Label Text Settings (Windows) affect how new captions and all atom labels for the current document are drawn and formatted. Changing the Text Settings in the Text Settings dialog box (Macintosh, Figure 1-10), or Caption/ Label Text Settings (Windows, Figure 1-11), affects the current document only.

When you change settings for captions, all new captions you create will use the new settings, previously drawn labels are not changed. When you change settings for atom labels, all new atom labels you create will use the new settings, but all previously drawn atom labels will be scaled to a size that is proportional to the new size. This scaling method prevents atom labels specifically sized to be proportional relative to another atom label to lose this relationship.

You can save text settings in Stationery Pad documents (Macintosh) or Style Sheets (Windows) if you repeatedly use the same settings. See Chapter 4, Captions and Atom Labels, and “Saving Customized Settings” later in this chapter..

Fractional Character Widths (Macintosh Only): Choose the Fractional Character Widths checkbox to change the spacing between characters so that they are as close to proportional spacing as possible. If you are printing to a PostScript printer this option generally improves the font appearance. The screen image of the font is also affected by this checkbox, and the text may look irregular on the screen.

NOTE: If you copy structures to other applications, make sure the character widths setting is the same in the other application or else printing problems may occur.


Color Palette

Choose Color Palette to display a dialog box where you can add, remove, or change the default foreground and background color and specify the other colors available for coloring objects.

Changes made to the color palette affect the current document only. You can save Color Palette settings in a Style Sheet/Stationery Pad. For more information see "Saving Customized Settings" later in this chapter.

A summary of each of the options is described in Table 1-7.

Table 1-7 Color Palette options

Click this button	If you want to...
New Color	add a new color box and set its color using the Color Picker or Color Wheel dialog box.
Set Color	change the color associated with a color box that you have selected in the left side of the dialog box. Any objects using the old color are changed to the new color.
Remove Color	delete a color box that you have selected in the left side of the dialog box. Any objects using the removed color are changed to the Foreground color.


Saving Customized Settings

Every new document created within ChemDraw uses a Style Sheet/Stationery Pad to obtain its document settings. Style Sheets/Stationery Pads can also contain predefined objects. When you create a new document, you actually create an untitled copy of the Style Sheet/Stationery Pad. You can make any changes you want to the copy of the Style Sheet without affecting the Style Sheet/Stationery Pad itself. By creating different Style Sheets/Stationery Pads, you can avoid the need to specify the document settings repeatedly when you switch between projects that require different settings. As a convenience, Style Sheets/Stationery Pads can be stored in the cd_items directory (Windows) or ChemDraw Folder (Macintosh) so that they are accessible from the Open Special submenu in the File menu.


Applying Settings From Other Documents

To apply document settings to the active window that are contained in a Style Sheet located in the cd_items directory/ChemDraw Folder:

•	From the File menu, choose Apply Settings.

•	From the Apply Settings submenu, choose a Style Sheet/Stationery Pad.

The settings in the active document window change to those found in the Style Sheet/Stationery Pad that you choose.

To apply the document settings contained in a ChemDraw document or Style Sheet/Stationery Pad not contained in the cd_items directory (Windows) or ChemDraw Folder (Macintosh) to the document in the active window:

•	From the Apply Settings submenu, choose Other.

The Open dialog box appears.

•	Select a ChemDraw document or Style Sheet/Stationery Pad and click the OK or Open button.

The Apply Settings command specifically preserves any style differences within a document. For example, if you have one short and one long bond in your original document, you will still one short and one bond after you have chosen the Apply Settings command, even if the lengths of the bonds are different.

To make different bonds within one document the same length, you must either scale them individually or use the Clean Up Structure command. For more information, see “Resizing Objects” in Chapter 7, Working with Selections, and “Structure Cleanup” in Chapter 8, Advanced Drawing Techniques.

NOTE: n ChemDraw Pro, Template Style Sheets/Stationery Pads don’t appear in the Apply Settings pop-up menu. However, you can access Template Style Sheets/Stationery using the Other command. In the ChemDraw Plug-in, templates may not be edited.


Menu Extension DLLs (Windows Only)

Through the ChemOffice SDK (Software Developers Kit), new menus and menu items that control ChemDraw can be added to ChemDraw. At this time, the SDK requires a solid working knowledge of C or C++ programming for implementing these menu extensions.

For more information about the SDK see our web page at: http://www.camsoft.com.


Script (Macintosh only)

The Scripts menu contains scripts that you can use to perform tasks within ChemDraw or between ChemDraw and another scriptable application.

Scripts found in the Scripts menu are created using Apples Script Editor application. With the proper script extensions in conjunction with Apples Script Editor application, you can create scripts using the AppleScript scripting language and add scripts to the Scripts menu by placing them in the ChemDraw Folder.

NOTE: Scripts not stored within the ChemDraw Folder are not accessible from the Scripts menu.

To read about the scripts that come with ChemDraw:

From the Scripts menu, Choose Read About ChemDraw.

To learn more about AppleScript and the Script Editor application see your system manuals. There is also a variety of manuals and guides available from various sources that discuss AppleScript in more detail.

NOTE: The Scripts menu will not be active if you do not have any Scripts within your ChemDraw Folder. AppleScript 1.1 or later is required to use the scripts supplied with ChemDraw.


Chapter 2, Getting Started Tutorials - Overview
Overview

This chapter provides several tutorials designed to teach you useful drawing techniques.

You should review the section "Conventions" in the Introduction of this help file. The terminology found there is used throughout these tutorials. You may also find it useful to have your Quick Reference card handy as you perform each tutorial.


Tutorial 1: Reaction Schemes

In this tutorial, you will draw the following (simplified) reaction scheme:

·	First, start ChemDraw.

·	From the File menu, choose Save As.

·	In the text box at the bottom of the dialog box, type "tut1.cdx".

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Click the OK button (Windows) or the Save button (Macintosh).

·	Open the Tools menu and make sure there is a check mark next to the Fixed Lengths and Fixed Angles command. If either command is not checked, choose the command again to select it.

NOTE: Applying fixed lengths and fixed angles assists you in creating structures with bond lengths and angles that are consistent with each other. The fixed length is set in the Drawing Settings dialog box. The fixed angle is always an increment of 15 degrees.

1.	Select the Solid Bond tool by clicking its icon.

1. click

2.	Position the pointer (which appears as a cross when a bond tool is selected) anywhere in a document window and hold down the mouse button.

3.	Drag the mouse diagonally upwards to the right.

2. point		3. drag
Release the mouse button when you have made a 30 degree angle and extended the bond to its fixed length (look at the Message area at the lower left corner of the document window).

NOTE: When drawing with bond tools, you must always draw the first bond in a structure by dragging as shown above. You cannot begin a structure by clicking using a bond tool or by adding a bond to a caption. If you are using a ring tool, you can click to begin a structure.

Next, add a bond:

4.	Point to the right atom of the bond.

5.	Click the atom to add a bond.

A second bond is deposited forming a 120 degree angle between the bonds.

NOTE: The angle used when clicking to add bonds is controlled by the Chain Angle setting in the Drawing Settings dialog box in the File menu. If this bond angle cannot be established, the next smaller and logical bond angle is used.

4. point		5. click
Next, add a second bond:

6.	Continue pointing to atom C2.

7.	Click the atom to add a bond.

6. point		7. click
Next you will change a single bond into a double bond:

8.	Point to C2 and hold the mouse button down.

9.	Drag from C2 to C4 over the existing single bond. Release the mouse button.

8. point		9. drag
Next you will add labels to the structure. Atom labels can be added in several ways. These will be illustrated in various steps in the tutorial.

10.	Point to atom shown below.

11.	Double-click the atom.

10. point		11. double-click
12.	Type "O" in the text box that appears.

To close the text box you can click in an empty area of the window or click another tool to select it.

12. type

In the next series of steps you will learn how to duplicate a structure and create another structure from the duplicate.

First, you will select the structure:

13.	Select the Lasso tool by clicking its icon.

13. click

The last structure drawn is automatically selected. Next, you will create the duplicate.

14.	Point over the Selection rectangle.

15.	Press and hold down the Ctrl key (Windows) or the Option key (Macintosh).

The pointer turns to a hand with a plus sign inside to signal that you are in the duplication mode of a selection tool.

14. point		15. press Ctrl (or Option)
16.	Drag the Selection Rectangle to the right.

A copy of the structure is created when you begin dragging. The original structure remains in its original position. Release the mouse button when the copy is clear of the original.

16. drag
TIP: When you create a copy in the manner just shown you can drag it anywhere in the document window. However, you may want to restrict the position of the copy so it remains aligned with the original. To do so, simply hold down the Alt key (Windows) or Command key (Macintosh) in addition to the modifier key mentioned in the last step.

Next, you will modify the duplicated structure.

17.	Select the Solid Bond tool by clicking its icon.

17. click

18.	Point to atom shown below.

19.	Click the atom to add a bond.

18. point		19. click
To add several bonds to a single atom:

20.	Point to the atom shown below.

21.	Click the bond three times, allowing a pause in between each click.

NOTE: If you click too fast, the click will be interpreted as a double-click, and a text box will open, or a triple-click which will repeat your last atom label.

20. point		21. click
NOTE: The angle used when bonds are deposited in this way is based on the Chain Angles Setting in the Drawing Settings dialog box. If that value cannot be established the next chemically logical angle is used. If you need to reorient one of the bonds that you created, hold down the Shift key and point to a non-attached atom and drag the atom to another position.

To reposition one of the bonds:

22.	Hold down the Shift key and point at the vertical bond that is facing downwards.

23.	Drag the bond so that it is facing diagonally to upwards to the right.

Release the mouse button and depressed keys.

22. Shift + point		23. drag
Next you will create an atom label using one of the easiest methods, HotKeys. Many of the keys on your keyboard have been preassigned to be HotKeys and are linked to specific atom labels.

24.	Point to atom shown below.

25.	Press the lowercase "o" key on your keyboard.

When you use HotKeys that represent a single element, like "O", the proper number of hydrogens are added to the label. To see this, click the double bond with the Eraser tool. To continue with this tutorial, choose Undo from the Edit menu.

24. point		25. press "o"
In the next step you will use a selection tool to move the structures apart from one another to make room for adding an arrow. A new method for selecting is introduced.

At this point in the tutorial you should have two structures within your window.

TIP: Now that you have all the structures for the reaction scheme, you can check that you have drawn them correctly by using the Check Structure command. ·	Select a selection tool. The last structure drawn is automatically selected. To select a different structure, double-click one of its bonds. ·	Choose Check Structure from the Structure menu. A message indicating whether errors were found or not will appear. ·	Repeat for the other structure.

NOTE: If an error is found, you can click the Stop button in the message window that appears to highlight the troubled portion of the structure.

26.	Select the Marquee tool by clicking its icon.

26. click

NOTE: Alternatively, you can select the lasso tool and hold down the Option key (or Ctrl key) to use the Marquee model.

28.	Drag diagonally over the entire structure.

Once you have dragged over the objects, release the mouse button and the depressed keys to create the selection.

27. Ctrl (or Option) + point		28. drag
Next, you will drag the selection to make room for adding an arrow.

29.	Hold down the Alt key (Windows) or Command key (Macintosh) to constrain movement of the selection and drag the Selection Rectangle.

29. Alt (or Command) + drag

Next you will add arrows to a reaction scheme.

30.	Hold down the mouse button over the Arrow tool to display the Arrow palette.

NOTE: The triangle in the lower left corner of the Arrow icon indicates it contains a palette.

31.	Drag the cursor to the small normal arrow (first row, third column).

Once you have selected an arrow you can release the mouse button.

NOTE: Once you have chosen an arrow from the palette it becomes the default arrow type. You can use that arrow by clicking the Arrow tool to select it. You only need to display the arrow palette if you want to change to a different arrow type.

30. press and hold		31. drag
Next you will draw using the arrow you selected.

32.	Point to the end of the reactant and hold the mouse button down.

33.	Drag the Arrow to the length you want.

When you have the length you want, you can release the mouse button.

Tip: If you need to alter the length (or the angle relative to the X axis) of the arrow after you draw it: ·	Hold down the Shift key and point to the arrowhead (a highlight box appears when you are pointing correctly). ·	Drag the arrowhead to the length (and angle) you want.

32. point between the structures

33. drag

Adding line formula or other captions for representing reagents and/or reaction conditions is performed using the Text tool. As pointed out earlier, the Text tool has two functions, labeling atoms and creating captions. To use the Text tool for creating captions and line formula, point to an empty area of the document window (i.e. don't point at an atom). The pointer will appear as an insertion point indicating that a caption will be created if you click the mouse button.

34.	Click the Text tool to select it.

34. click

35.	Point above the arrow.

36.	Click to create a text box.

35. point		36. click
37	Type "OH".

37. type

NOTE: Captions and line formula with subscript numbers can be created by choosing the Formula style from the Text menu. In addition, formula style allows you to calculate information about a caption using the Analyze Structure command.

NOTE: To realign the caption if necessary, select a selection tool and drag the caption.

Next you will add a charge symbol. Rather than add a negative charge symbol using the keyboard, there are specialized symbols available in the Reaction Mechanism tool palette.

38	Click and hold down the mouse button over the Chemical Symbol tool.

39	Hold down the mouse button and drag to the circled negative charge symbol (second row, fourth column) and release the mouse button.

38. click and hold		39. drag
Next you will draw a symbol using the one you selected from the palette:

40	Position the pointer to the right of the OH caption.

41	Click to deposit the charge symbol.

Move the cursor away from the symbol after you have drawn it.

40. point		41. click
It is often convenient to make several related objects selectable by double-clicking for purposes of manipulating or moving. Any objects added from the Chemical Symbols palette is automatically associated with the structure (or caption in formula style) that it is closest to. However, objects such as arrows are not associated automatically. You can manually group objects using the Group command.

To group several objects:

42.	Select a selection tool by clicking its icon.

42. click

43.	Hold down the Shift key and click the arrow, the OH caption and the charge symbol.

43. Shift + click each object

The Shift key allows you to add objects to a selection without deselecting other objects.

NOTE: If you are holding down the Shift key and click an already selected object, that object is deselected.

·	From the Object menu, choose Group.

NOTE: Objects within a group are still selectable as individual objects by single clicking.

Next, you will use the Text tool to create a caption containing the name and amount of reactant, and center the information under the structure.

44.	Click the Text tool to select it.

44. click

45.	Point below your first structure.

46.	Click to create a text box.

45. point		46. click
47.	From the Text menu, choose Centered.

The orientation of the "I" beam changes to the center of the text box (Macintosh). The default that appears whenever you create a new text box is flush left.

47. choose Centered

Next, type your caption:

48.	Type "2-propanone".

49.	Press the Return key to begin a new line.

48. type		49. press Return
50.	Type "2 moles".

50. type

Next you will create an aligned caption for the other structure.

51.	Press the Tab key to create another Text box that is aligned adjacent to the first.

52.	Type "4-hydroxy-4-methyl-2-pentanone", press Return and type "1 mole".

NOTE: Using the Tab key in the caption mode of the text tool provides a way of creating tables of captions. As an added benefit, the font, size and style (not the justification which is flush left by default) are maintained from the previous caption.

51. press Tab

TIP: If your captions are not aligned properly beneath the structures you should move them using a selection tool. ·	Click a selection tool to select it. The text box is automatically selected since this was the last object you drew. ·	Press the Left or Right Arrow key to move the caption so it is centered beneath structures. This method will maintain the alignment created by the Tab key.

To complete the presentation, you can add a shadowed box around the scheme:

53.	Hold down the mouse button over the Drawing Elements tool.

54.	Select the shadowed box from the palette of drawing elements.

53. press and hold		54. drag
53.	Point to the upper left corner of the reaction scheme.

54.	Hold down the mouse button and drag diagonally downward to the left to draw the box.

When the box encompasses the entire reaction scheme release the mouse button.

53. point

54. drag

·	From the File menu, choose Save.

Your changes are saved.

·	From the File menu, choose Close.

You have completed your first reaction scheme. In the next exercise you'll add an intermediate to make the scheme more complete.


Tutorial 2: Drawing an Intermediate

This tutorial will show you how to draw the following intermediate structure starting from a ring and add arrows with customized shapes using the Pen tool:

·	From the File menu, choose New Document.

·	From the File menu, choose Save As.

·	In the text box at the bottom of the dialog box, type "tut2.cdx".

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Click the OK button (Windows) or the Save button (Macintosh).

1.	Select the Cyclohexane Ring tool.

1. click

2.	Point in an empty area of a document window.

3.	Click to deposit a ring.

2. point		3. click
Next you will erase some of the bonds in the ring:

4.	Select the Eraser tool.

4. click

5.	Point to the atom between the apex bonds.

TIP: You can also delete these bonds individually by pointing at the center of a bond and clicking.

6.	Click the atom to delete the atom and its bonds.

5. point		6. click
Next you will add a bond:

7.	Select the Solid Bond tool.

7. click

8.	Point to atom C2.

9.	Click to add a bond.

8. point		9. click
Next you will add a second bond:

10.	Move the cursor over C4.

11.	Click to add another bond.

10. point		11. click
Next you will add a third bond using a dragging method to make sure it has the desired orientation:

12.	Continue to keep the cursor on C4.

13.	Hold down the mouse button and drag upward to the right.

When the bond is oriented, release the mouse button to deposit the bond.

12. point		13. drag
Next you will create a double bond:

14.	Point to C2.

15.	Drag from C2 to C3 over the existing bond to create a double bond.

14. point		15. drag
Next you will change orientation of the lines of the double bond:

16.	Point to the center of the double bond.

17.	Click (don't drag) to move the second bond to the outside.

Note, you can move a double bond in this manner whenever a bond tool is the selected tool. Notice that the cursor takes on the appearance of the bond tool that is selected.

16. point		17. click
Next, you will add an atom label.

18.	Point to the atom to label.

19.	Double-click the atom to open a text box.

18. point		19. double-click
20.	Type "O", choose superscript from the Style Submenu in the Text menu and then type "-".

20. type

Next, you will label an atom with "OH":

21.	Point to the rightmost atom.

22.	Double-click the atom to open a text box.

21. point		22. double-click
23..	Type "OH".

23. type

Now you need to add some arrows to indicate electron flow; however, the arrows in the arrows palette are too uniform for this purpose. Instead you can create customized arrows using the Pen tool.

24.	Click the Pen tool.

25.	Set the style of the curve to an arrow, by choosing Arrow at End from the Curves menu.

24. click

26.	Point the cursor near the double bond where you want to indicate the start of electron flow.

27.	Drag downwards and to the left. Release the mouse button.

The cursor changes to a hand with a "+" in it indicating that you are in the editing mode of the Pen tool.

26. point		27. drag
28.	Position the cursor where you want the arrow head to appear.

29.	Drag upwards to create a curve segment.

Press the Escape key (to exit drawing mode). The lines around the curve will then disappear.

28. point		29. drag
Next you will refine the shape of the arrow:

30.	Point at the center of the curve until a highlight box appears.

31.	Click the curve to enter edit mode.

30. point		31. click
32.	Point to the handle pointing away from the curve to the right (this is called a tangent handle and controls the tangent of the curve that it touches)

33.	Drag the handle upwards to the left to make the arrow head point more inward.

Press the Escape key when the arrow is how you want it.

32. point		33. drag
34.	Create additional arrows in the same manner and create a proton caption to complete the intermediate.

result

TIP: While working with arrows or other objects that are in small places, you can magnify your view using the Magnify command in the Tools menu.

·	From the File menu, choose Save.

·	From the File menu, choose Close.


Tutorial 3: Using Rings

In this tutorial you learn how to draw more complex structures by using rings:

·	From the File menu, choose New Document.

·	From the File menu, choose Save As.

·	Type "tut3.cdx" in the text box.

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Click the OK button (Windows) or the Save button (Macintosh).

1.	Select the Cyclohexane Ring tool.

1. click

2.	Point in an empty area of a document window.

3.	Click to deposit a ring.

2. point		3. click
Next, you will fuse a second ring to the first:

4.	Point to the center of lower right bond in the ring.

5.	Click to fuse another ring.

4. point		5. click
Next, you will fuse a third ring:

6.	Point to the ring shown below.

7.	Click to fuse another ring.

You should end up with the structure shown on the right.

6. point		7. click
Finally, you will fuse a fourth ring:

8.	Point to the ring shown below.

9.	Click to fuse another ring.

8. point		9. click
Next you will remove bonds in the ring using the Eraser tool.

10.	Select the Eraser tool.

10. click

11.	Point to the atom between the upper two bonds.

Highlight boxes appear on the bonds that will be removed.

12.	Click to delete the atom and its bonds.

11. point		12. click
13.	Continue deleting by clicking each of the atoms or bonds shown below. You should end up with the structure shown on the right.

13. click		result
Next you will add double bonds to the structure and realign them.

14.	Select the Solid Single Bond tool.

14. click

15.	Point to the atom indicated below.

16.	Drag upwards to draw a double bond.

15. click		result
Next, add another double bond:

16.	Point to the atom indicated below

17.	Drag upwards to draw a double bond.

16. point		17. drag
Next you will realign the double bonds so they are centered.

18.	Point to the center of the lower double bond.

19.	Click to move the line to the other side of the bond. Click again to center the bonds.

18. point		19. click twice
20.	Point to the center of the upper double bond.

21.	Click to move the line to the other side of the bond. Click again to center the bonds.

20. point		21. click twice
Next you will add a carbon atom label:

22.	Point over the atom to label as carbon.

23.	Press the "c" key on your keyboard. This key is a Hotkey assigned to the atom label "C".

The atom label will be appear with the correct number of hydrogens.

22. point		23. press "c"
Next you will add an oxygen atom label to complete the structure:

24.	Point over the atom to label as oxygen.

25.	Press the "o" key on your keyboard. This key is a Hotkey assigned to the atom label "O".

24. point		25. press "o"
·	From the File menu, choose Save.

·	From the File menu, choose Close.


Tutorial 4: Fischer Projections

This tutorial shows you how to draw a Fischer projection of glucose (shown below) by drawing a linear series of bonds.

·	From the Open Special submenu in the File menu choose ACS-1996.cds (Windows) or from the Windows menu choose ACS Document 1996 (Macintosh).

The new document created is based on a Style Sheet (Windows), or Stationery pad (Macintosh).

You might notice in this example that bonds and atom label fonts/sizes are different. These special documents allow you to have pre-configured settings for different tasks. In this example, the ACS template is used to help maintain information for a one- column layout (a Page Setting), for bonds with a Fixed length of 0.2 inches (a Drawing Setting), and for Atom Labels in Times Font (a Text Setting). This is the desired setting for structures to be published in all ACS journals Choosing document.cds (Windows) or document (Macintosh) will create a document with the settings shipped with ChemDraw.

·	From the File menu, choose Save As.

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Type "tut4.cdx" in the text box at the bottom of the Save dialog box.

·	Click the OK button (Windows) or Save button (Macintosh).

1.	Select the Solid Bond tool.

1. click

2.	Point in the document window.

3.	Hold down the mouse button and drag vertically to draw your first bond.

2. point		3. drag
Next, add another bond:

4.	Point to the lower atom.

5.	Hold down the mouse button and drag downward to draw the second bond.

4. point		5. drag
6.	Repeat above step 4 and 5 three more times for a total of five bonds.

NOTE: Drag the pointer along the length of the bonds you drew, you will see the pointer alternate between an arrow and a cross. The arrow indicates you are pointing over the center of a bond, and the cross indicates you are pointing to an atom.

6. point and drag three more times

Next, you will add a horizontal bond to the second atom in the string of bonds you created:

7.	Point to C2.

8.	Click the atom to add a perpendicular bond.

7. point		8. click
Next, add a horizontal bond in the opposite direction:

9.	Continue pointing to C2.

10.	Click the atom to add a perpendicular bond in the opposite direction.

9. point		10. click
Next you will add a bond to the next atom in the line of bonds.

11.	Point at the third atom (C3).

12.	Click the atom to add a perpendicular bond.

11. point		12. click
13.	Continue pointing to C3.

14.	Click the atom to add a perpendicular bond in the opposite direction.

13. point		14. click
15.	Repeat steps 13 and 14 for the for the fourth (C4) and fifth (C5) atoms.

15. click C4 and C5 twice
Next, add a label to C1:

16.	Point to C1.

17.	Double-click C1 to create a text box, then type CHO.

16. point		17. click and type
18.	Point to C6.

19.	Double-click C6 to create a text box, then type CH2OH. Click outside the text box to close it.

18. point		19. click and type
Next add the H, and OH labels:

20.	Point to the atom shown below.

21.	Press the key "h" to label the atom with a Hydrogen.

20. point		21. press "h"
22.	Repeat this labeling procedure for the remaining atoms that are hydrogen indicated by arrows below on the left.

22. point and press "h"		Result
Next, label the OH's:

23.	Repeat this labeling procedure for the remaining atoms pressing the Hotkey "o" to label them with OH. The result should appear as shown below.

result
As a final step, you will check the chemical syntax of the structure you drew followed by automatically calculating the formula and molecular weight.

24.	Select a selection tool to automatically select the last structure drawn. If the structure is not selected for whatever reason, double-click the structure.

25.	From the Structure menu, choose Analyze Structure.

If drawn correctly, a dialog box with information calculated from the structure appears (if errors are present, a check structure message appears indicating the problem).

26.	In the dialog box that appears, deselect all but the Formula and Molecular Weight checkboxes.

27.	Click the Paste button to paste the information as a caption below the structure.

28.	Click outside the caption to deselect it.

result

·	From the File menu, choose Save.

·	From the File menu, choose Close.


Tutorial 5: Perspective Drawings

In this exercise you will learn how to create perspective drawings by drawing D-glucose as a Haworth projection.

·	From the File menu, choose New.

NOTE: The new command will be appended with the last Stationery Pad/Style Sheet used. If you are working from tutorial 4, the name of the command will be New ACS-1996 (Windows) or New ACS Document 1996 (Macintosh).

·	From the File menu, choose Save.

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Type "tut5.cdx" in the text box at the bottom of the dialog box.

·	Click the OK button (Windows) or the Save button (Macintosh).

1.	Select the Cyclohexane ring tool.

1. click

2.	Point in an empty area of a document window.

3.	Click to deposit a ring.

2. point		3. click
4.	Press Ctrl+ Alt+Tab keys (Windows) or Command+Tab key (Macintosh) to automatically select a selection tool and the last structure drawn.

4. press Ctrl+Alt+Tab or Command+Tab
5.	Point to the upper right corner of the Selection Rectangle (the Rotation handle).

NOTE: The cursor changes to a curved double-sided arrow indicating the rotation mode of a selection tool is activated.

6.	Drag the Rotation handle to the right about 30 degrees (look at the Messages area at the lower left of the window).

5. point and drag		6. result
NOTE: Even though you have fixed angles on, the angle is not constrained. Fixed angles only applies when you are drawing with the tool used to create it. For example, if you had created this ring by dragging rather than clicking, the angle you could use would be constrained if Fixed Angles is on. Try it out!

7.	Click outside the structure to deselect it.

8.	Point to the atom indicated below on the left.

9.	Press the HotKey "o".

8. point		9. type "o"
Next, add vertical bonds:

10.	Click the Single Bond tool to select it.

10. click

11.	Point to C1 (to the right of the oxygen)

12.	Drag upwards to create a bond.

11. point		12. drag upward
13.	Point to C1 again

14.	Drag downwards to create another bond.

13. point		14. drag downwards
15.	Repeat for C2 through C4 as indicated by the arrows in the lower left illustration. The result will appear as the right illustration.

16. point		result
Next, draw one upwards bond at C5:

17.	Point to C5.

18.	Hold down the mouse button and drag upwards.

17. point		18. drag upwards
For the downward bond for C5, you will need to turn Fixed lengths off. Otherwise, the bond will be joined to the upward bond of C3. You can temporarily disable Fixed lengths using a modifier key.

19.	Point to C5.

20.	Hold down the Alt key (Windows) or Command key (Macintosh), then hold down the mouse button and drag downward from C5. Stop dragging about half the distance to the upward bond on C3.

19. point		20. drag downwards
Next you will distort the structure to change its aspect ratio. This will give the perspective of viewing the structure along the Z-axis.

21.	Select the Lasso tool by clicking its icon.

20. click

22.	Point to the Resize handle(lower right corner) and hold down the Alt key (Windows) or the Command key (Macintosh).

NOTE: The cursor changes to a cross with arrows at each end indicating the distortion function of a selection tool is activated.

23.	Drag upwards until you have distorted the structure to about 50% (shown in the Messages area of the window).

22. press Command key or Alt key and point		23. drag upwards
Next you will create OH labels. Since this label is repeatedly used, you will learn how to repeat a label. Only labels where you have opened a text box will be repeatable.

24.	Select the single bond tool, point to the atom shown on the left and double-click to open a text box.

25.	Type OH, and move the pointer to the next atom as shown and triple-click to repeat the atom label.

24. press Command key or Alt key and point		25. double-click and type "OH"
26.	Triple-click the remaining atoms (as shown below) to repeat the OH label.

NOTE: You can choose the Magnify command from the tools menu is you find it difficult to place the labels.

26. triple click to repeat labels
Next, add the CH2OH label:

27.	Triple click the upper atom of C5.

28.	Next, press the Return key to open the atom label text box and type CH2 before the OH.

NOTE: This last step showed you another HotKey, namely the "Return" key, that opens a text box for the last atom labeled. The definition for this particular HotKey cannot be changed.

28. label CH2OH

In this final step you will change the type of the frontmost bonds.

29.	Click the bold bond tool.

29. click

30.	Point to the center of the frontmost bond

31.	Click to change to the new bond type.

30. point to bond's center		31. click
NOTE: Notice that the cursor changes to a bold arrow as you point at the bond.

32.	Click the Solid Wedge bond tool.

32. click

33.	Point to the bond to the right of the bond you changed.

34.	Click slightly off center in the direction that you want the wide end of the wedge to be oriented, then click.

34. click the center of each of the bond's indicated		result
NOTE: If the highlight box disappears, you have moved the pointer too far. You may want to magnify your view using the Magnify command in the Tools menu if you find it difficult to place the pointer where you want.

NOTE: If the wedge is pointed in the wrong direction, click the bond again to flip its orientation.

·	From the File menu, choose Save.

·	From the File menu, choose Close.


Tutorial 6: Newman Projections

This tutorial shows you how to draw a Newman projection.

·	From the File menu, choose New.

NOTE: This command will read "New ACS Document 1996" if you just completed the last tutorial.

·	From the File menu, choose Save As.

·	Select a directory (Windows) or folder (Macintosh) in which to save the file.

·	Type "tut6.cdx" in the text box and click the Save button (Macintosh) or OK button (Windows).

1.	Click the Solid Bond tool to select it.

1. click

2.	Point in the document window.

3.	Drag downwards to create the first bond.

2. point		drag
4.	Continue pointing at the lower atom.

5.	Click again to add a second bond.

4. point		5. click
6.	Continue pointing at the same atom

7.	Click again to add a third bond.

6. point		7. click
8.	Select the Lasso tool by clicking its icon.

The last structure you drew is automatically selected.

8. click

9.	Point within the Selection rectangle, Hold down the Ctrl key (Windows) or Option key (Macintosh).

10.	Hold down the mouse button and drag a copy of the structure diagonally upward to the right of the original.

9. point and press Ctrl key or Option key		10. drag
11.	Release the mouse button (and depressed key) when the copy is positioned.

Next you will add a bond between the duplicated structures:

12.	Click the Solid Bond tool to select it.

12. click

13.	Point to the central atom of the lower fragment. Hold down the Alt key (Windows) or Command key (Macintosh).

14.	Hold down the mouse button and drag to the central atom of the upper fragment.

Release the mouse button when the highlight box over the central atom appears.

13. point and press Alt key or Command key		14. drag
NOTE: The modifier key used in this step removes the fixed length constraint so you can draw a longer bond that will reach the upper fragment. Fixed angles are also disabled.

This example is not using an orbital as an orbital. Instead, you will use the Orbital tool to draw the hollow circle that is particular to Newman Projections.

15.	Hold down the mouse button over the Orbital tool to display its palette.

16.	Drag to the unfilled s orbital (first column, first row).

15. press and hold		16. drag
17.	Point to the left center carbon, hold down the Alt key (Windows) or Command key (Macintosh).

18.	Hold down the mouse button and drag outward. Notice that a highlight box doesn't appear over the atom. The orbital tool does not change as if you were adding bonds or atoms to the structures. Thus, you may want to group the orbital with the structure to make it moveable as a unit.

NOTE: The size of the orbital is constrained just like bonds. The constraint is based on a percentage of the Fixed length setting in the Drawing Settings dialog box.

NOTE: Whenever you want to add orbitals to a structure, you drag starting from the atom that you want to position the center or node.

17. point		18. drag
Next you will move part of the structure to the front so overlap the orbital:

19.	Click the Lasso tool.

19. click

20.	Point above the structure

21.	Hold down the mouse button and drag around the upper fragment to select the three bonds

NOTE: Only bonds that are completely within the Lasso area are selected. You don't want the bond connecting the two fragments to be selected. If you find this difficult to do with the lasso, you may wish to Shift+click on each bond separately.

20. drag		21. result
Next, you will rotate the selection:

22.	Double-click the Rotation handle in the upper right of the Selection Rectangle to open the Rotate dialog box.

23.	Type 180 in the text box and click the Rotate button.

22. point and double click		23. type 180 and click Rotate
Next, you will change the layering of the structure so that the selection is frontmost.

24.	From the Object menu, choose Bring to Front.

24. choose Bring to Front
Finally, you will orient the frontmost part of the structure to create a Newman projection.

25.	Point within the Selection Rectangle until the pointer changes to a hand.

26.	Drag the selection until the central atom of the selection is centered within the orbital. Release the mouse button and click outside the Selection Rectangle to deselect the structure.

25. point		26. drag
·	From the File menu, choose Save.

·	From the File menu, choose Close.


Chapter 3, Drawing Chemical Structures - Overview
Overview

At the heart of ChemDraw are tools specially designed for drawing chemical structures: nine bond tools, ten ring tools, and an acyclic chain tool. This chapter describes how to create chemical structure drawings using these tools.


Single Bonds

Nine bond tool icons are located in the Tools palette. The icons representing each tool are shown below (Table 3-1):

Table 3-1 Single bond tool icons

	Solid Bond
	Dashed Bond
	Hashed Wedged Bond
	Bold Wedged Bond
	Hashed Bond
	Bold Bond
	Hollow Wedged Bond
	Wavy Bond
	Dative Bond
More:

Selecting a Bond Tool

Drawing Bonds

Dative Bonds and Wedged Bonds

Message Area

Adding Bonds by Dragging


Selecting a Bond Tool

To select a bond tool:

·	Click a bond tool icon in the Tools palette.

Figure 3-1 Selecting a bond tool

click


Drawing Bonds

You can draw bonds that are either constrained to a fixed length or have variable lengths. You can also draw bonds with a fixed or variable angle relative to the X axis.

More:

Fixed Lengths

Fixed Angles

Drawing Unconstrained Bonds

Shortcut - Toggling Fixed Length and Fixed Angle


Fixed Lengths

To draw bonds that are constrained to a fixed length:

•	From the Tools menu, choose Fixed Lengths.

A check mark appears next to the Fixed Lengths command indicating that it is turned on. When Fixed Lengths is turned on, all the bonds drawn are constrained to the fixed length specified in the Drawing Settings dialog box.

·	Select a bond tool.

·	Drag from one end of the bond to the other.

Figure 3-2 Drawing the first bond

point		drag
The Message area at the bottom left of a document window shows the length and angle of the bond as you drag. The bond will not extend further than the fixed length. Also see "Message Area" later in this chapter for further information.

Drawing Settings Guide

Fixed Length

Bonds drawn when Fixed Length in the Tools menu is turned on are constrained to the value set in the Fixed Length box in the Drawing Settings dialog box.

To change the Fixed Length value:

·	Choose Drawing Settings from the File menu.

·	Type a value in the Fixed Length text box and click the OK button.

This change affects newly drawn bonds in the current document only. See “Saving Customized Settings” in Chapter 1, ChemDraw Basics to learn how to make the change permanent.


Fixed Angles

To draw bonds that are constrained to angles that are multiples of 15 degrees relative to the X axis:

·	From the Tools menu, choose Fixed Angles.

A check mark appears next to the Fixed Angles command indicating that it is on.

·	Select a bond tool by clicking its icon.

·	Drag from one end of the bond to the other in a document window.

The Message area indicates that the bond angle is constrained to 15 degree increments. Also see "Message Area" later in this chapter.


Drawing Unconstrained Bonds

To draw a bond that is not constrained to a fixed length or fixed angle:

·	From the Tools menu, choose Fixed Lengths and Fixed Angles if they are presently checked.

The absence of a check mark next to the Fixed Lengths or Fixed Angles command in the Tools menu indicates the commands are off.

·	Select a bond tool by clicking its icon.

·	Drag from one end of the bond to the other in a document window.

You can draw any bond length and create any angle relative to the X axis. The Message area displays the length of the bond and the angle it makes with the X axis as you drag the bond.


Shortcut - Toggling Fixed Length and Fixed Angle

To temporarily toggle Fixed Lengths and Fixed Angles on and off:

·	Alt+drag (Windows) or Command+drag (Macintosh) from one end of a bond to the other end in the document window.

If Fixed Lengths or Fixed Angles are turned on, you can hold down the Alt key (Windows) or the Command key (Macintosh) to temporarily turn off these constraints.


Dative Bonds and Wedged Bonds

Wedge Bond:orientation ;Dative bonds and wedged bonds are drawn with a specific orientation in a document window.

To draw a dative bond:

·	Select the Dative Bond tool.

Figure 3-3 Dative bond tool

click

·	Drag from the positive to the negative end (arrow head) of the dative bond.

Figure 3-4 Drawing a dative bond

point		drag
To draw a wedged bond:

·	Select one of the wedged bond tools.

Figure 3-5 Wedged bond tool

click

·	Drag from the narrow end of the wedged bond to the wide end of the wedged bond.

Figure 3-6 Drawing a wedged bond

point		drag
If the orientation of the dative bond is not what you want:

·	Click the center of the dative or wedge bond using its tool.

The orientation of the bond is inverted.


Message Area

As you draw bonds, information appears in the Message area at the lower left corner of a document window. The message area in Figure 3-7 shows the bond length and angle the bond makes with the x-axis

Figure 3-7 Message area

The number on the left indicates the length of the bond you are drawing. The number on the right indicates the counterclockwise angle between the bond and the positive X axis.

Preferences Guide

Units

The units used in the Rulers, Crosshair and Drawing Settings can be can set to centimeters, inches, or points.

To change the units:

·	From the File menu, choose Preferences.

·	Choose a unit measurement from the Units pop-up menu, then click the OK button.

This change affects all documents.

More:

Adding a Bond by Clicking


Adding a Bond by Clicking

To quickly add a fixed length bond:

·	Select a bond tool by clicking its icon.

·	Click an atom.

Figure 3-8 Adding a bond by clicking

Point		click
A new bond is drawn and is joined to the atom you clicked. Bonds drawn by this method are always drawn using the Fixed Length specified in the Drawing Settings dialog box. The angle that the deposited bond makes with its nearest neighbor is equal to the Chain Angle set in the Drawing Settings dialog box. If this angle cannot be established, a smaller angle is used.


Adding Bonds by Dragging

To control the orientation of bonds that you draw, you can add bonds by dragging

·	Select a bond tool.

·	Point to an atom.

A highlight box appears over the atom indicating where the bond will be joined (if you are pointing to a bond, the highlight box encompasses the entire bond).

·	Drag from the atom at which you are pointing to the end of the new bond.

If Fixed Lengths is turned on, the length of the bond will be constrained. If Fixed Angles is turned on the angle will be constrained to 15 degree increments.

A new bond is drawn and joined to the atom where the highlight box appeared. By using this dragging method for drawing the bond, you can control the orientation of the other end of the bond.

Figure 3-9 Adding a bond by dragging

point		drag
Preferences Guide

Tolerance

The size of highlight box is controlled by the value in the box labeled "Tolerance" in the Preferences dialog box. The default setting for the Tolerance is 5 pixels. This means, for instance, that the highlight box appears on atoms if the pointer is located in a square region 10 pixels on a side or +/- 5 pixels from the atom.

To change the Tolerance:

·	From the File menu, choose Preferences.

·	Click the up or down Tolerance control arrow to increase or decrease the tolerance, then click the OK button.


Multiple Bonds

You can use the Solid, Dashed, and Bold Bond tools to create the following multiple bonds:

Table 3-2 Types of multiple bonds

	Double
	Tautomeric
	Aromatic
	Double Bold
	Triple
	Double Either
More:

Double Bonds

Double Either Bonds

Triple Bonds


Chapter 3, Drawing Chemical Structures - Multiple Bonds - Double Bonds
Double Bonds

To draw a double bond:

·	Select the Solid, Dashed or Bold bond tool.

·	Drag over an existing bond from one end of the bond to the other end.

A double bond is created.

Figure 3-10 Drawing a double bond

point		drag


Double Either Bonds

To create a double either bond:

·	Draw a double bond using the Solid Single bond tool.

·	Select the Wavy bond tool.

·	Point to the center of the double bond and click.


Triple Bonds

You can draw a triple bond by drawing another single bond on top of a double bond.

To draw a triple bond:

·	Select any bond tool.

·	Drag from one end of an existing double bond to the other.

All bonds in a triple bond are solid bonds.

To change a triple bond into a single bond:

·	Select any bond tool.

·	Drag from one end of an existing triple bond to the other.

The triple bond changes into a single bond that corresponds to the tool you used to draw over the bond. Another way to reduce the bond order is to use the Eraser tool. See "Eraser Tool" in Chapter 7, Working with Selections.

Figure 3-11 Drawing a triple bond

point		drag


Ring Tools

There are ten ring tools available for drawing various ring sizes and types:

Table 3-3 Available ring tools

	Cyclopropane Ring Tool
	Cyclobutane Ring Tool
	Cyclopentane Ring Tool
	Cyclohexane Ring Tool
	Cycloheptane Ring Tool
	Cyclooctane Ring Tool
	Cyclohexane Chair Ring Tool (1)
	Cyclohexane Chair Ring Tool (2)
	Cyclopentadiene Ring Tool
	Benzene Ring Tool
NOTE: If you are using a small monitor, such as found on the Macintosh SE/30, several of the Cycloalkane Ring tools are grouped into a pop-up palette.

More:

Selecting a Ring Tool

Drawing a Ring

Cyclohexane Chair Ring Tools

Resonance Delocalized Rings

Cyclopentadiene and Benzene Ring Tools


Selecting a Ring Tool

To select a Ring tool:

·	Click a Ring Tool icon in the Tools palette.

Figure 3-12 Selecting the cyclohexane ring tool

click


Drawing a Ring

To draw a ring:

·	Select a Ring tool.

·	Position the pointer in a document window.

When you point in a document window, the pointer changes to a ring tool pointer (as shown in Figure 3-13). The highlight box on the ring tool pointer indicates the atom that is drawn first. The bond directly below the highlight box is the bond that is drawn first.

Figure 3-13 Ring tool cursor (enlarged)

·	Drag from the beginning to the end of the first bond.

If Fixed Lengths is on when you draw a ring, the length of each bond in the ring is automatically set to the fixed length. If Fixed Angles is on, the angle the first bond in the ring makes with the X axis is restricted to 15 degree increments. See "Drawing Bonds with Fixed Lengths and Fixed Angles" earlier in this chapter for more information.

Figure 3-14 Drawing a cyclohexane ring

point		drag
More:

Depositing a Ring by Clicking


Depositing a Ring by Clicking

To quickly draw a ring:

·	Select a Ring tool and click in a document window.

A ring appears in a document window centered around the pointer. The ring is drawn using the Fixed Length specified in the Drawing Settings dialog box. The ring is deposited in the orientation shown on the ring tool icon.

If you click a bond, the ring is fused to that bond. If you click an atom, the ring is attached to that atom, if the atom is in a ring, a spiro-linkage is formed. If you click in an empty area in the document window, the ring is centered around that point.

Figure 3-15 Adding a cyclohexane ring

Point		click

Figure 3-16 Fusing a cyclohexane ring

point		click

Figure 3-17 Creating a spiro linkage

point		click


Cyclohexane Chair Ring Tools

The cyclohexane chair ring tools can be drawn in two orientations (Figure 3-18). Using the methods previously discussed, the chair is drawn in a horizontal orientation.

To change a cyclohexane chair ring to a vertical orientation:

·	Select one of the Cyclohexane Chair Ring tools.

·	Shift+drag from the beginning of the first bond to the end of the bond or, Shift+click in a document window.

Figure 3-18 Shift key effect on cyclohexane chair rings orientation

Without Shift Key		With Shift Key


Resonance Delocalized Rings

.Any of the ring tools, except the cyclohexane chairs, can be drawn in a resonance delocalized form.

To draw a resonance delocalized ring:

·	Select a Ring tool.

·	Hold down the Ctrl key (Windows) or the Option key (Macintosh) and drag or click to draw the ring.

A circle appears inside the ring.

Figure 3-19 Option key effect on ring tool drawing

Without Ctrl or Option key		With Alt or Option key
NOTE: The circle is automatically grouped with the ring when drawn. For a discussion of grouping objects, see "Grouping" in Chapter 7, Working with Selections.


Cyclopentadiene and Benzene Ring Tools

The double bonds in the cyclopentadiene or benzene ring tools can be drawn in either of two orientations.

Normally, the first bond drawn is a double bond. This is the orientation indicated on the cyclopentadiene and benzene ring tool pointer. You can draw in this orientation by the methods previously discussed.

To shift the orientation so that the first bond drawn is a single bond:

·	Shift+drag from the beginning of the first single bond to the end of the single bond.

·	Or, Shift+click in a document window to deposit the bond with a Fixed Length.

In Figure 3-20, the arrow indicates the direction the first bond is drawn.

Figure 3-20 Shift key effect on benzene right orientation

Without Shift Key		With Shift Key


Acyclic Chains

Using the Acyclic Chain tool, you can draw long hydrocarbon chains.

Figure 3-21 The Acyclic chain tool

click

More:

Selecting the Acyclic Chain Tool

Drawing an Acyclic Chain

Adding Chains


Selecting the Acyclic Chain Tool

To select the Acyclic Chain tool:

·	Click the Acyclic Chain Tool icon in the Tools palette.


Drawing an Acyclic Chain

To draw an acyclic chain:

·	Click the Acyclic chain tool to select it.

·	Drag in the direction you want the chain to grow in a document window.

A number appears at the end of the chain indicating how many bonds you have drawn.

When Fixed Lengths is on, the pointer on the acyclic chain can be dragged to make any angle relative to the X axis. At a constant chain length, the position of the first bond, and all subsequent odd-numbered atoms will depend on the direction you drag. Before releasing the mouse button, this position can be changed by dragging in the opposite direction. When Fixed Angles is on, the angle the acyclic chain can make relative to the X axis is constrained to 15 degree increments. The internal angle between the bonds of the chain is specified by the Chain Angle spin button in the Drawing Settings dialog box.

Figure 3-22 Drawing a chain by dragging

point		drag


Adding Chains

To add an Acyclic Chain to an existing atom:

·	Select the Acyclic Chain tool.

·	Point to the atom to which you want to attach the chain.

·	Drag in the direction you want the chain to grow.

Figure 3-23 Adding a chain to an existing atom

point		drag
To specify a chain length:

·	Select the Acyclic Chain tool.

·	Click an existing atom or an empty area in a document window.

The Add Chain dialog box appears.

·	Type the number of bonds in the chain.

·	Click the Add button.

To add another chain of the same length anywhere in a document window:

·	Ctrl+click (or Option+click) an existing atom or click in an empty area within the document window.

Drawing Settings Guide

Chain Angle

All of the bond angles in an acyclic chain are equal. The size of this angle is controlled by the Chain Angle value in the Drawing Settings dialog box. The angle is measured in degrees. You can set the angle at any integral value between 1 and 179 degrees.

To change the chain angle:

·	Select Drawing Settings from the File menu.

·	Click the up or down Chain Angle control arrow to increase or decrease the angle.

·	Click the OK button.

This change affects the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics to learn how to make the change permanent.


Drawing Settings for Bonds

There are four Drawing Settings that affect the appearance of bonds: Line Width, Bold Width, Hash Spacing, and Bond Spacing. These settings apply simultaneously to all the bonds in the active document. Changes made to any of these settings affect the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics.

Drawing Settings Guide

Line Width

The thickness of all bonds, lines and arrowheads is specified in the box labeled "Line Width" in the Drawing Settings dialog box.

0.5 Point	1 Point	1.5 Point

To change the Line Width:

·	From the File Menu, choose Drawing Settings.

·	Type a value in the Line Width box, then click the OK button.

Bold Width

The thickness of bold, hashed and wedged bonds is specified in the box labeled "Bold Width" in the Drawing Settings dialog box.

2 point	4 Point	8 Point

To change the Bold Width:

·	Enter a bold width in the Bold Width box, then click the OK button.

The Bold Width setting must be greater than the Line Width setting.

This change affects the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics to learn how to make the change permanent.

Hash Spacing

The spacing between the hash marks in hashed bonds and the dash marks in dashed arrows in curves is specified in the box labeled "Hash Spacing" in the Drawing Settings dialog box.

2 Point	2.5 Point	3 Point

To change the Hash Spacing:

·	Type a Hash Spacing in the Hash Spacing box, then click the OK button.

Bond Spacing

The spacing between bonds in double and triple bonds is measured as a percentage of the bond length. It is specified using the Bond Spacing control arrows in the Drawing Settings dialog box. You can set the bond spacing from 1 to 100% of the bond length.

10%	14%	18%

To change the bond spacing:

·	Click the up or down Bond Spacing arrow to increase or decrease the bond spacing.

This change affects the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics to learn how to make the change permanent.


Editing Bonds

You can modify the appearance of chemical structures by changing bond types, moving atoms, and layering bonds.

More:

Changing Bond Types

Orientation of Wedged and Dative Bonds

Alignment of Double Bonds

Moving Atoms

Bond Crossings


Changing Bond Types

To change a single bond from one type to another:

·	Select a bond tool.

·	Point at the center of an existing bond and click.

The bond that you click changes to the new bond type.

Figure 3-25 Changing a bond type

point to bond's center		click and move cursor away
More:

Double Bonds


Chapter 3, Drawing Chemical Structures - Changing Bond Types - Double Bonds
Double Bonds

To change one type of double bond to another:

·	Select the Bold, Dashed or Solid Bond tool.

·	Point to one of the bonds in the double bond.

·	Click the bond.

The double bond changes to the new bond type. One of the bonds in the double bond is always a solid or dashed bond. Note, if you click a Tautomeric bond (solid/dashed) a second time with the dashed bond tool, you create an aromatic double bond (dashed/dashed).

Figure 3-26 Changing the bond type of a double bond

point to bond's center		click and move cursor away


Orientation of Wedged and Dative Bonds

When you draw or change a bond to a wedged or dative bond, the orientation of the bond is chosen appropriately. However, if the orientation is the opposite of what you want:

·	Click the dative or wedged bond with the tool used to create it.

The dative or wedged bond is changed to the opposite orientation.

Figure 3-27 Changing the orientation of a wedged bond

wedge in wrong orientation		point at bond's center and click


Alignment of Double Bonds

The bonds in a double bond can have any one of three alignments relative to other bonds: above, below or centered.

Figure 3-28 Alignment of lines in double bonds

above	below	centered

To change the alignment of a double bond:

·	Select the bond tool used to create the existing double bond.

·	Click the center of the double bond.

The double bond shifts so that one of the lines of the bond moves to the other side of the structure.

·	Click one line of the double bond again to change to the next alignment.

Figure 3-29 Changing the alignment of a double bond

pointing		click (and move cursor away)


Chapter 3, Drawing Chemical Structures - Editing Bonds - Moving Atoms
Moving Atoms

 To move an atom in a chemical structure:

·	Select a bond tool.

You can use any of the bond tools to move an atom within acyclic or cyclic structures (you cannot use a ring tool to perform this type of operation).

·	Point at the atom to move.

A highlight box appears over the atom.

·	Shift+drag the atom.

If you move an atom that has only one bond attached to it while Fixed Lengths is on, the atom will rotate around the other atom of the bond; the bond will not lengthen or shorten. If you move an atom that is part of two or more bonds, the atom will follow the pointer whether or not Fixed Lengths is on, and the bonds will stretch.

Figure 3-30 Moving an atom

point at atom		Shift + drag
If you drag one atom on top of an adjacent atom, the bond between the atoms disappears. This is useful for converting a 6-membered ring into a 5-membered ring.

Figure 3-31 Moving an atom onto another

point at atom and Shift Drag		Release when one atom is on another
NOTE: In addition to moving an atom with a bond tool, you can also move atom(s) using a selection tool.


Bond Crossings

When one bond crosses another, white space is used to indicate which bond is in front of the other.

To change which bond is in front:

·	Select any bond tool.

·	Double-click the bond that you want to bring to the front.

Figure 3-32 Changing the front to back ordering of a bond

point at bond		double-click
NOTE: You can also layer bonds using the Bring to Front and Send to Back commands. For a discussion of these commands, see Chapter 12, Working with Page Layout.

NOTE: You can magnify your view to make changing the bond layering easier. For more information, see "Perspectives" in Chapter 12, Working with Page Layout.

Drawing Settings Guide

Margin Width

To adjust the white space that surrounds a bond in the region where one bond crosses another:

·	Choose Drawing Settings from the File menu.

·	Enter a value in the Margin Width box.

·	Click the OK button.

The units used are those specified in the Preferences dialog box.

This change affects the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics to learn how to make the change permanent.


Chapter 4, Captions and Atom Labels - Overview
Overview

There are two kinds of text in ChemDraw: caption text and atom label text. Caption text is used to create annotations, chemical names, chemical formulas, page titles, and information in tables. Atom label text is used to identify atoms and substructures by their chemical symbols and formulas. Also see Chapter 8, Advanced Drawing Techniques, to learn how to use HotKeys to quickly label atoms, and how to check the chemistry of captions and atom labels.

Figure 4-1 Atom labels and captions

Both caption text and atom label text are created using the Text tool. The location of the created text, in empty space or on an atom, determines the type of text and the available justifications.

Figure 4-2 Text tool

click

To select the Text tool:

·	Click the Text Tool icon in the Tools palette.

Text in a single caption or atom label can be edited using the Text tool. Other manipulations, especially those done simultaneously on several captions or atom labels, can be performed using a selection tool. To learn more about a selection tool, see Chapter 7, Working with Selections.

Two useful shortcuts when working with text are as follows:

To quickly switch from the Text tool to a selection tool:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh).

The text box is automatically selected when you switch to a selection tool.

To quickly switch from a selection tool to the Text tool when a caption or atom label is selected:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh).

The Text tool is selected and the text box is opened for editing.

To select multiple atom labels or captions with a selection tool:

·	Shift+click the atom labels or captions.

Preferences Guide (Macintosh)

Use Bitmap Fonts When Available

When text appears in a document on the screen, it can appear using either a bitmap or a TrueType font. To use Bitmap fonts if they are available:

·	From the File menu, choose Preferences.

·	Select the Use Bitmap Fonts When Available checkbox.

Text drawn using Bitmap fonts looks better and appears more quickly than text drawn using TrueType fonts. However, the size and position of text drawn using Bitmap fonts will change somewhat when printed. For accurate correspondence between what you see on the screen and what is printed, deselect Use Bitmap Fonts When Available. This change affects all documents.


Chapter 4, Captions and Atom Labels - Captions
Captions

To create a caption:

·	Select the Text tool.

·	Point in an empty space in a document window.

A Caption text box with a flashing insertion point appears.

Figure 4-3 Creating a text box

point		click
·	Type a caption.

The text box widens as you type to accommodate the caption.

·	To create a new line, press the Enter (or Return) key.

You can also click outside the Caption text box in a document window to close the current Caption text box and open a new Caption text box.

NOTE: You can verify the chemical significance of captions using the Check Structure command. See Chapter 8, Advanced Drawing Techniques, for more information. In addition, you can use the Analyze Structure command to calculate information about the caption. See Chapter 8, Advanced Drawing Techniques, for more information. Captions must be formatted in "Formula" style for these commands to work for captions.

Preferences Guide

Require Ctrl+Enter (or Option+Return) to Create New Line

Within a Caption text box, the standard way of creating a new line is to press the Enter (or Return) key. To close the text box you need to click anywhere outside the text box, press the Enter key (or Return key) or select another tool. If you prefer to use the Return key to close the Caption text box, and create a new line by pressing Ctrl+Enter (Windows) or Option+Return (Macintosh), do the following:

·	From the File menu, choose Preferences.

Under the option "Require Ctrl+Enter (or Option+Return) to Create New Line"

·	Select the Captions check box and click the OK button.

This change affects all documents.

More:

Caption Width

Editing the Contents of a Caption

Caption Fonts, Sizes and Styles

Caption Justification and Line Spacing


Caption Width

To change the width of a caption:

·	Select a caption using the Text tool.

The Caption text box appears around the caption. On the right side of the text box is a Resize handle.

Figure 4-4 Text box resize handle

·	Drag the Resize handle.

The point at which the text wraps is adjusted as you drag the Resize handle.


Editing the Contents of a Caption

To open a caption for editing:

·	Select the Text tool.

·	Point at a caption and click to open the text box.

The caption text is highlighted within the Caption text box.

Figure 4-5 Selecting captions for editing

point		click
To open a caption for editing by using a selection tool:

·	Select a single caption using a selection tool.

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh).

·	Or, select the Text tool.

The Text tool is selected and the caption is opened. If more than one caption is selected, all captions are deselected.

To change all of the highlighted text within an open text box:

·	Type the new caption text over the highlighted text.

The highlighted text disappears as you type the new caption.

Figure 4-6 Replacing selected text

select		type
If not all the text is highlighted, and you want to select all of the caption text:

·	From the Edit menu, choose Select All.

To change part of the caption text:

·	Drag the insertion point over a part of the caption.

Figure 4-7 Replacing part of the text

point		drag
NOTE: You can use the Delete key (or the Forward Delete key if available) to delete the character directly after the Insertion point. On the Macintosh, you can also delete a word directly after the Insertion point by pressing Option+Forward Delete.


Caption Fonts, Sizes and Styles

Each new caption that you create has the Font, Size and Style that is specified in the Text Settings dialog box. You can change these settings so that all new captions you type will use these new values, or you can change individual captions by using the commands in the Text menu.

To change the Font, Size or Style for an entire caption, or for several captions:

·	Select the caption(s) using a selection tool.

To change only a part of a single caption you must use the Text tool:

·	Select part of the caption with the Text tool.

More:

Caption Font

Caption Size

Style


Caption Font

To specify a font for a selected caption:

·	From the Font submenu within the Text menu, choose a Font.


Caption Size

To change the size for a selected caption text:

·	From the Size submenu within the Text menu, choose a Size.

If the size you want is not listed in the Size submenu:

·	From the Size submenu, choose Other.

·	Type a number in the Other Size dialog box.

·	Click the OK button.

Only one alternate size is listed in the Size menu. This alternate size changes depending on the selection.

NOTE: If the captions you select have more than a single font or size, a hyphen appears next to each font or size that is contained within the selection. Choosing a new font or size in this instance will change all of the selected text to the new font or size.


Style

The Style submenu contains three items in addition to those found normally in the Macintosh Style menu: Superscript, Subscript, and Formula. The Superscript style reduces the font size of caption text by twenty-five percent and raises its baseline. The Subscript style reduces the caption text by twenty-five percent and lowers the baseline. When you apply the Formula style, numbers are subscripted automatically, for instance, C6H6.

To specify the style of caption text:

·	From the Style submenu within the Text menu, choose a style.

You can apply several styles to the same selected caption(s), for instance, Formula, Bold and Italic. You can also apply multiple styles to different portions of a single caption.

NOTE: If the captions you select have more than one style, a hyphen appears next to each style that is not applied to the entire selection. A checkmark appears next to each style that applies to all of the selected text. Making a choice (except for Plain) in this instance will add the new style choice to all of the selected captions. Previously applied styles are not affected.

Text Settings Guide

New Caption Font, Size and Style

To change the font, size and styles for new captions:

·	From the File menu, choose Text Settings.

·	Choose a Font, Size and Style in the section labeled "New Captions".

These settings take effect for all new captions that you type in the current document window. To use these settings in new documents you can save them in a Stationery Pad. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics.

This change affects the current document only. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics to learn how to make the change permanent.


Caption Justification and Line Spacing

All new captions you create are Flush Left and the line spacing is chosen automatically unless you specify otherwise by using the Justification and Line Spacing commands in the Text menu. All text in a single caption must have the same Justification and Line Spacing. There are four justifications available in the Text menu: Flush Left, Centered, Flush Right, and Justified. Flush Left creates left-justified caption text; Centered creates centered caption text; Flush Right creates right-justified caption text; and Justified creates right-left justified caption text.

Figure 4-8 Text justification

Flush Left		Centered
Flush Right		Justified
To specify the justification of caption(s):

·	Select a caption(s) using a selection tool.

·	From the Text menu, choose a justification.

To specify the spacing between different lines of a caption:

·	Select a caption(s) using a selection tool.

·	From the Text menu, choose Line Spacing.

The Line Spacing dialog box appears.

There are three ways to specify the Line Spacing: Automatic, Variable, and Fixed. Caption text with automatic line spacing has consistently spaced lines of text; the spacing is based on the size of the largest character in the caption. Captions with variable line spacing have lines of text with different spacing. In this case, the spacing is based on the largest character in each line. Captions with fixed line spacing have consistently spaced lines that you specify. Unless you specify otherwise, caption text has automatic line spacing.

To specify Automatic or Variable line spacing:

·	Select the Automatic or Variable button.

To specify a Fixed line spacing:

·	Select the Fixed button.

·	Type a value in the text box labeled "Fixed at".

NOTE: The line spacing of ChemDraw version 2.x documents opened within ChemDraw version 4.0 is automatically set to Fixed Line spacing to maintain vertical alignment.


Chapter 4, Captions and Atom Labels - Atom Labels
Atom Labels

To place an atom label on an atom:

·	Select the Text tool.

·	Point to an atom.

The pointer changes when it is positioned correctly over an atom to indicate that you will create an atom label rather than a caption.

·	Click the atom.

An Atom Label text box appears over the atom.

Figure 4-10 Creating an atom label

point		click
·	Type an atom label.

Numbers are automatically subscripted. Letters in an atom label are positioned on a bond depending on the justification you have chosen (see "Atom Label Justification" later in this chapter). Numbers, leading open parentheses and trailing closed parentheses are ignored in the positioning of atom labels.

·	Press Enter (or Return) to close the Atom Label text box.

You can also click outside the current Atom Label text box on another unlabeled atom to open a new Atom Label text box.

To label an atom using a bond or ring tool

·	Point to an atom and double-click.

Figure 4-11 Creating an atom label using a bond tool

point		double-click
NOTE: As an alternative to creating atom labels using the Text tool, you can use HotKeys to label atoms. In addition, you can label atoms using Nicknames which are text representations of substructures. You can also verify the chemical significance of atom labels using the Check structure command. See "Nicknames" in Chapter 8, Advanced Drawing Techniques, for more information.

Preferences Guide

Require Ctrl+Enter (Windows) or Option+Return (Macintosh) to Create New Line

In an Atom Label text box, the standard way of creating a new line is to hold down the Ctrl key (Windows) or Option key (Macintosh) and press the Enter (or Return) key. To close the text box, press the Enter (or Return) key. If you prefer to use the Enter (or Return) key to add a new line and to close the Atom Label text box by clicking outside the text box. you can change this preference as follows:

·	From the File menu, choose Preferences.

·	Deselect the Atom Labels check box (under this option).

·	Click the OK button.

This change affects all documents.

More:

Isotopes

Charges

Repeating an Atom Label

Editing Atom Labels

Deleting an Atom Label

Atom Label Justification

Atom Label Line Spacing


Chapter 4, Captions and Atom Labels - Atom Labels - Isotopes
Isotopes

ChemDraw will automatically recognize isotopes1 if they are properly labeled with superscripts, e.g., 13C, 15N, and 81Br.

To label an atom with an isotope:

·	Open a text box on an atom position using the Text tool or by double-clicking with a Bond tool.

·	Type an isotope, e.g. "13C".

·	Using the Text tool, select the isotopic mass, "13".

·	From the Text menu, in the Style submenu, select Superscript.

Copying and pasting will transfer this isotope information to the Clipboard.

NOTE: ChemDraw contains extensive information (reproduced by permission of CRC Press, Inc.) about known isotopes. It is extremely unlikely that you would ever need to change this information, but if you do, you may edit the Isotopes table (Macintosh) or Isotopes.txt (Windows) with your favorite text editor.

Figure 4-12 Creating an isotope label

Select		Choose Superscript
1Adapted from the Table of Isotopes data, in the CRC Handbook of Chemistry and Physics, 77th Ed., Lide, D.R., Editor-in-Chief, CRC Press, Boca Raton, Florida, ©1996. With permission.


Chapter 4, Captions and Atom Labels - Atom Labels - Charges
Charges

To label an atom with an associated charge:

·	Open a text box on an atom position using the Text tool or by double-clicking with a Bond tool.

·	Type a plus or minus sign after the atom you want to label with a charge.

·	(Optional) From the Style submenu in the Text menu, choose Superscript.


Repeating an Atom Label

To label several atoms with the same atom label:

·	Select the Text tool.

·	Label a single atom.

·	Double-click an atom to repeat the previous label.

Alternatively, you can label an atom while using a bond or ring tool:

·	Select a bond tool.

·	Double-click an atom.

To repeat the label:

·	Triple-click an atom to repeat the previous label.

This method can be used with any of the bond tools, ring tools and the Acyclic Chain tool.

Figure 4-13 Repeating an atom label

label an atom		point and triple-click (with a bond tool)
Atom labels are always in the frontmost object layer in the document window and are therefore always layered on top of bonds. See "Layering Objects " in Chapter 12, Working with Page Layout, for more information.

Drawing Settings Guide

Margin Width

The white space surrounding the atom label can be adjusted so that more or less of the attached bond is hidden.

To adjust the white space:

·	From the File menu, choose Drawing Settings.

·	Type a new value in the Margin Width box.

·	Click the OK button.


Editing Atom Labels

To edit an atom label:

·	Click an existing label using the Text tool or double-click using a bond or ring tool.

The highlighted atom label text appears within the Atom Label text box.

If the text is not all highlighted, and you want to select all of the atom label:

·	From the Edit menu, choose Select All.

To edit part of the atom label:

·	Drag the insertion point over part of the atom label.

·	Type the new characters.

·	Press Enter (or Return) to close the Atom Label text box.

You can also open an atom label for editing as follows:

·	Double-click an existing atom label using a bond, ring, or chain tool.

Figure 4-14 Opening a text box for editing

point (with a bond or ring tool)		double-click


Deleting an Atom Label

To delete an atom label, leaving the underlying bond(s) unchanged:

·	Click the atom label using the Eraser tool or use the "space" HotKey.


Atom Label Justification

With ChemDraw, you can use the Automatic, Centered, Flush Left, Flush Right, and Stacked Above justifications from the Text menu to create labels that identify atoms and functional groups in your chemical structure without obscuring any bonds or other atom labels. Below are examples of the atom label justifications available ("Justified" is not available for atom labels).

Figure 4-15a Atom Label justification

Stacked Above		Centered
Flush Left		Flush Right
More:

Automatic Justification

Stacked Above

Flush Left Justification

Flush Right Justification

Centered Justification


Automatic Justification

Atom labels can be justified automatically. To correctly position the atom label, the label is broken up into tokens. A token consists of an uppercase letter followed by any numbers or lowercase letters. The first token is attached to the atom and the rest of the label is positioned so that it does not obscure other parts of the chemical structure.

To create N-methylpiperidine, label an atom in cyclohexane with the atom label "NCH3", which contains the three tokens, "N" and "C" and "H3". If you label C3, the tokens are placed from left to right since there are bonds to the left of the atom. If you label C5, the tokens are placed from right to left since there are bonds to the right of the atom:

Figure 4-15b Creating N-methylpiperidine

Labeling C-3		Labeling C-5
In ChemDraw Pro, you can force an entire multi-atom label to be a token by defining it as a Nickname. This prevents the label from flipping when applied to the left side of a structure.

For instance, If you define the Nickname "CH3", and label C-5 with the combined label and nickname "NCH3", the final orientation will be "CH3N" rather than "H3CN". In this case, the Nickname, "CH3", is a token (also see "Nicknames" in Chapter 8, Advanced Drawing Techniques).

If you label C-1, the second and third tokens are placed above the first token since there are bonds below the atom. If you label C-4, the second and third tokens are placed below the first token.

Figure 4-15c Creating N-methylpiperidine

Labeling C-1		Labeling C-4

To turn off Automatic Atom Labels:

•	Select an atom label..

•	From the Text menu, choose a justification other than Automatic.

Preferences Guide

Automatic Atom Labels

To set the default atom label justification to Automatic:

·	From the File menu, choose Preferences.

·	Select the Automatic Atom Labels check box, then click the OK button.

Each time a new atom label is created, it will be automatically justified.

This change affects all documents.


Stacked Above

To create an atom label using the Stacked Above justification.

·	Select an atom to label.

·	From the Text menu, choose Stacked Above.

·	Type the top row of characters.

To create a new line:

·	Press Ctrl+Enter (or Option+Return) to create a new line.

·	Type the second line of characters.

The atom label appears as a stack.

·	Repeat this procedure until the entire stacked atom label is created.

To close the Atom Label text box:

·	Press Enter (or Return).

The bonds are drawn to the left-most character in the last row that you typed.

Figure 4-16 Stacked Above labels

Type label top down


Flush Left Justification

To create an atom label using the Flush Left justification:

·	Select an atom to label.

·	From the Text menu, choose Flush Left.

·	Type the first row of characters.

·	Press Ctrl+Enter (or Option+Return) to create a new line.

·	Repeat this procedure until you have typed all rows in the atom label.

·	Press Enter (or Return) to close the Atom Label text box.

Figure 4-17 Flush Left labels

Type label left to right

Preferences Guide

Automatic Atom Labels

To set the default atom label justification to be other than automatic:

·	From the File menu, choose Preferences.

·	Deselect the Automatic Atom Labels check box.

·	Click the OK button.

Each time a new atom label is created, it will be justified to the left, right, or stacked above, depending on the position of the bonds to that atom.

This change affects all documents.


Flush Right Justification

To create an atom label using the Flush Right justification:

·	Select an atom to label.

·	From the Text menu, choose Flush Right.

·	Type the first row of characters.

When an atom label is justified Flush Right, the last uppercase character in the first line you type will be attached to the bond.

·	Press Ctrl+Enter (or Option+Return) to create a new line.

·	Repeat this procedure until you have typed all the rows in the atom label.

·	Press Enter (or Return) to close the Atom Label text box.

Figure 4-18 Flush Right labels

Type label left to right


Centered Justification

 To create an atom label that has Centered justification.

·	Select an atom to label.

·	From the Text menu, choose Centered.

·	Type a row of characters so the center character is the character you want connected to the bond.

Centered justification requires that the same number of characters (including numbers) is on each side of the atom label joining the bond. For instance, CH3NCH3, will be centered on the nitrogen, whereas RNCH3 will be centered on the carbon.

·	Press Ctrl+Enter (or Option+Return) to create a new line, if necessary.

·	Type the second line of characters.

NOTE: for precise control of atom label alignment, see "Multi-attached Labels" in Chapter 8, Advanced Drawing Techniques.

Figure 4-19 Centered labels

Type label left to right


Atom Label Line Spacing

You can adjust the spacing between the lines of an atom label using the Line Spacing command in the Text menu in the same manner as for captions. Variable line spacing is the default for atom labels. Refer to "Caption Label Justification and Line Spacing" earlier in this chapter for a detailed discussion of the Line Spacing command and the associated options available in the Line Spacing dialog box.

NOTE: The line spacing of ChemDraw version 2.x documents opened within ChemDraw version 4.0 is automatically set to Fixed Line spacing to maintain vertical alignment.


Entering non-Roman Text

 ChemDraw uses standard methods for entering all types of text, including the Greek characters and other symbols that are common to chemistry. To enter Greek characters:

·	Click in a text box with the text tool

·	From the Font submenu in the Text menu, choose Symbol (Windows users may need to choose the Other menu item within this submenu, and select the Symbol font from there)

·	Enter your text. For example, an "a" is a lower-case alpha, a "P" is a capital pi.

·	If you want to enter additional non-Greek text in the same text box, go back to the Font submenu and re-select the font that was selected previously.

To enter a degree symbol:

·	Click in a text box with the text tool

Macintosh

·	Press option+shift+8

Windows

·	Make sure the Num Lock key is pressed on your keypad

·	Hold down the ALT key

·	On the keypad, type the four numbers 0,1,7,6 in succession

·	Release the ALT key

NOTE: The characters available differ in different fonts. A list of all characters available in each font -- and what to type to get them -- is available in the KeyCaps menu item of the Apple menu (Macintosh) or the Character Map application in your Accessories program group (Windows).


Text Format

ChemDraw uses default format settings that determine the font, size and style of captions and atom labels that you type. You can change the formatting by choosing new formats before you type, or by selecting text and applying the new formats after you type. The format can be changed in two ways:

1. Using the Font, Size, and Style submenus.

2. Using the Format dialog box (Windows only).

NOTE: In addition, the Style can be changed using the key combinations listed to the right of the style command in the Style submenu, and the Size of selected text can be changed using the Resize handle or Scale dialog box using a selection tool.

Alternatively, you can change the defaults for a particular document using the atom label or caption text settings commands. Changing atom label defaults affects all existing atom labels, as well as newly created atom labels within the active document. Changing caption defaults changes the format for all newly created captions in the active window.

More:

Using the Font, Size and Style Submenus

Using the Format Dialog Box (Windows Only)

Changing Default Settings


Using the Font, Size and Style Submenus

 The Font, Size and Style submenus located in the Text menu provides a quick way to change individual format options for captions and atom labels.

The Font submenu contains fonts installed in your system, and lists the most recently used fonts. An "Other" command provides a way to add a font that is not currently listed.

The Size submenu contains the font sizes available, and lists the most recently used sizes. An "Other" command provides a way to add a size that is not currently listed.

The Style submenu contains three additional baseline styles not normally found in Style menus: Superscript, Subscript, and Formula. The Superscript style reduces the font size of caption text by twenty-five percent and raises its baseline. The Subscript style reduces the caption text by twenty-five percent and lowers the baseline. When you apply the Formula style, numbers are subscript automatically, for instance, C6H6. The default for atom labels normally contains the Formula style.

To change the Font, Size or Style using a submenu:

·	Before you begin typing, choose the font style and size that you want from the submenus.

·	Or, select the caption(s) using a selection tool, or individual captions or atom labels with the Text tool.

·	From the Size and Font submenus, choose the font style and size.

NOTE: If the captions you select have more than a single font or size, a partial selection mark appears next to each font, size or style that is contained within the selection. Choosing a new font or size in this instance will change all of the selected text to the new font or size. Choosing a style will add the new style to all of the selected captions or atom labels without affecting styles previously applied.

If the Font you want is not currently displayed in the submenu:

·	From the Fonts submenu, choose Other.

The Font dialog box appears.

·	From the Font drop-down list box, choose a font.

·	Type a number in the Other Size dialog box.

·	Click the OK button.

If the Size you want is not currently displayed in the submenu:

·	From the Size submenu, choose Other.

The Size dialog box appears.

·	Type a number in the Other Size dialog box and click the OK button.


Using the Format Dialog Box (Windows Only)

 The Format command in the Text menu displays a dialog box where you can make several format changes at one time, rather than choosing individual formats from submenus.

To change the font, size and style using the format dialog box.

·	Before you begin typing, choose Format from the Text menu.

·	Or, select the multiple captions or atom labels using a selection tool, or individual captions or atom labels with the Text tool.

·	From the Text menu, choose Format.

The Format dialog box appears.

·	Select the Font, Size and Style options that you want to apply.

·	Click the OK button.

The new formats are applied to the selection or to the new text you type.


Changing Default Settings

The default settings for caption and atom labels are changed using the Caption Text Settings and Label Text Settings commands in the File menu. The default settings are stored in the active document only. To use these settings in other documents you can save them in a Style Sheet. See "Saving Customized Settings" in Chapter 1, ChemDraw Basics.

Text Settings Guide

New Caption Font, Size and Style

To change the default font, size and styles for new captions:

·	From the File menu, choose Caption Text Settings.

The Caption Text Settings dialog box appears.

·	Select a Font, Size and Style.

These settings take effect for all new captions that you type in the active document window.

Atom Label Fonts, Size and Styles

To change the font, size and styles for all atom labels in the active document window (as well as any atom labels you create later):

·	From the File menu, choose Atom Label Text Settings.

The Atom Label Text Settings dialog box appears.

·	Select a Font, Size and Style.

Changing the size of atom labels in the Text Settings dialog box changes the size of each atom label in the active document window by the following scale factor:


Tables

With ChemDraw you can create tables of text using the Tab key in conjunction with the Text tool.

More:

Creating the First Row (column headings)

Creating a New Row

Adjusting Column Spacing

Adjusting Row Spacing

Moving Around Within Tables

Inserting a New Row


Creating the First Row (column headings)

To create the first row and establish the columns of a table:

·	Select the Text tool.

·	Click in a document window where you want the table to start.

·	Choose a style, font and size from the appropriate submenu in the Text menu and then type a caption.

·	Press Tab.

A second caption text box appears.

·	Choose a style, font and size from the appropriate submenu in the Text menu and then type a second caption.

The second column is placed 20 points (20/72 inch, 0.71 cm) to the right of the first.

·	Press Tab again to create a third column, and so on.

NOTE: The style, font and size that you set in each column will be maintained in all the rows that follow. For example, if column one is bold and column two is italic, the next row will automatically have column one as bold and column two as italic.

The following diagram illustrates the creation of new columns using the Tab key.

Figure 4-21 First row

To change the spacing between columns while editing a caption:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh) or select a selection tool.

The caption is automatically selected with a selection tool.

·	Press Right (or Left) ArRow.

This moves the selected caption to the right (or left) 1 point at a time.

To move 10 points at a time:

·	Press Ctrl+Right (or Left) Arrow (or Option+Left Arrow).

To return to the Caption text box after completing the spacing change:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh) or select the Text tool.

To create another column with this same spacing as the previous:

·	Press Tab.

A third caption text box appears, and so on.


Creating a New Row

To start a new row that is exactly aligned with the first:

·	Press Tab twice at the end of a Row.

A caption text box appears exactly aligned under the first caption positioned exactly 20 points below the first caption in the first Row.

The following diagram illustrates the creation of a new Row.

Figure 4-22 Creating a new row

To change the spacing between rows as you create the table:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh) when you are editing the first caption in a row, or, select a selection tool.

The caption is automatically selected with a selection tool.

·	Press the Down (or Up) ArRow.

This moves the selected caption downwards (or upwards) 1 point at a time.

To move 10 points at a time:

·	Press Ctrl+Down (or Up) Arrow (or Option+Arrow key).

To return to the Caption text box after completing the spacing change:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh) or select the Text tool.

To continue and fill in the row with captions:

·	Press Tab to create another caption in the row, then press Tab twice to begin a new Row.

The spacing between the newest row and the row directly before it will have the same spacing that you specified between the previous two rows.


Adjusting Column Spacing

You can also use a selection tool to adjust the column spacing as follows:

·	Select all of the captions in a column using a selection tool.

To change the spacing relative to the previous caption:

·	Alt+drag (Windows) or Command+drag (Macintosh) the caption(s).

Holding down the Alt key (Windows) or Command key (Macintosh) constrains the movement to the X axis so that you can maintain the row alignment.


Adjusting Row Spacing

You can also use a selection tool to adjust the row spacing as follows:

·	Select a selection tool and select all caption in a Row.

To change the spacing between the selected row and the previous row:

·	Alt+drag (Windows) or Command+drag (Macintosh) the captions down.

Holding down the Alt key (Windows) or Command key (Macintosh) constrains the movement to the Y axis so you can maintain the column alignment.


Moving Around Within Tables

To move around within an existing table.

·	Select the Text tool and select a caption.

To move to the caption on the right and open it for editing:

·	Press Tab, or, press Alt+Right Arrow (Windows) or Command+Right Arrow (Macintosh).

To move to the caption on the left and open it for editing:

·	Press Shift+Tab, or, press Alt+Left Arrow (Windows) or Command+Left Arrow (Macintosh).

To move to the caption below and open it for editing:

·	Press Alt+Down Arrow (Windows) or Command+Down Arrow (Macintosh).

To move to the caption above and open it for editing:

·	Press Shift+Alt+Enter (or Shift+Command+Return), or, Press Alt+Up Arrow (Windows) or Command+Up Arrow (Macintosh).


Inserting a New Row

To insert a row:

·	Select a selection tool and select a row of captions.

·	Alt+drag (Windows) or Command+drag (Macintosh) the selected Row.

The Alt key (Windows) or Command key (Macintosh) constrains the movement to the Y axis to maintain the column alignment.

·	Select the first caption in the row above or below the space you created.

·	Ctrl+Alt+drag (Windows) or Option+Command+drag (Macintosh) to create a copy of the caption and position it in the empty space you created.

The placement of this copied caption sets the position of the inserted Row.

To fill in the inserted row with caption text:

·	Select the Text tool and select the first caption in the inserted row, and type new text.

·	Press Tab to move to the second caption in the inserted row, and so on.


Chapter 5, Drawing Orbitals and Chemical Symbols - Overview
Overview

This chapter discusses two tools, the Orbital tool and the Chemical Symbols tool, that you can use to add to your structures. Both tools contain a palette of objects from which you can choose.


The Orbital Tool

The orbital tool is used to add orbitals to your chemical structures.

Orbitals are drawn so that its node appears first. To illustrate where the node for each orbital is, the remainder of this section illustrates each of the tools.

Figure 5-1 Orbital tool

Each orbital type is available in several fill patterns: white, gray, and black. Gray orbitals appear with grayscale shading on color and grayscale monitors and print with grayscale shading from PostScript printers when the Color/Grayscale option is selected in the Print dialog box.

Each orbital type is discussed separately below. While you draw an orbital, its length and angle relative to the X axis appears in the Message area.

You can constrain the length of an orbital by turning Fixed Lengths on in the Tools menu. You can also constrain the angle of all orbitals to 15 degree increments relative to the X axis by turning on Fixed Angles.

NOTE: Orbitals are not part of the structure they are drawn near, and are therefore not selected if you double-click a bond, atom or atom label with a selection tool. To group the orbitals with the structure, use the Group command in the Object menu.

More:

s-orbitals

sigma -orbitals

Single Lobe Orbitals

p-orbitals

Hybrid-orbitals

d-orbitals

dz2-orbitals


s-orbitals

To draw an s-orbital:

·	Point to an atom where the orbital will be centered.

·	Drag outward.

Figure 5-2 s-Orbitals

Figure 5-3 Adding an s-orbital

point		drag


s -orbitals
σ -orbitals

To draw a σ orbital:

·	Point to an atom where the orbital will be centered.

·	Drag outward along the long axis of the orbital.

Figure 5-4 σ-Orbitals


Single Lobe Orbitals

Single lobe orbitals are commonly used for indicating a lone pair. To draw a single lobe orbital:

·	Point to an atom where the narrow end of the orbital is to be attached.

·	Drag from the narrow end of the lobe to its wide end.

Figure 5-5 Single lobe orbitals

Figure 5-6 Adding a single lobe orbital

point		drag


p-orbitals

To draw a p-orbital:

·	Point to an atom where the node of the orbital is to be attached.

·	Drag from the orbital node to the wide end of the filled lobe.

Figure 5-7 p-Orbital icons

Figure 5-8 Drawing a p-orbital

point		drag


Hybrid-orbitals

To draw a hybrid orbital:

·	Point to an atom where the node of the orbital is to be attached.

·	Drag from the orbital node to the wide end of the major lobe of the orbital.

Figure 5-9 Hybrid orbitals


d-orbitals

.To draw a d-orbital:

·	Point to an atom where the node of the orbital is to be attached.

·	Drag from the center of the orbital to the wide end of a filled lobe.

Figure 5-10 d-Orbitals


dz2-orbitals

To draw a dz2-orbital:

·	Point to an atom where the node of the orbital will be attached.

·	Drag from the center of the orbital to the wide end of a lobe.

Figure 5-11 dz2-Orbitals


The Chemical Symbol Tool

 The Chemical Symbol tool is used to add chemical symbols to your structure.

Figure 5-12 Chemical Symbol tool

All chemical symbols are automatically grouped with the structure (or caption in formula style) to which it is closest. In addition, the symbols are included in any Analyze Structure or Check Structure function that you perform. See Chapter 7, Working with Selections, for more information about the Analyze and Check Structure command.

More:

H_dot and H_dash

Lone Pair

Radical

Radical Cation and Radical Anion

Charges

Stereochemical Flags

Free Sites

Editing a Symbol


H_dot and H_dash
H-dot and H-dash

To represent a hydrogen that is coming out of the plane toward you along the Z axis, use the H-dot symbol. To represent a hydrogen that is directed backwards into the plane away from you along the Z axis, use the H-dash.

Figure 5-13 H-dot and H-dash

To draw an H-dot or an H-dash:

·	Click an atom.

H-dots and H-dashes can only be drawn by clicking atoms.

Figure 5-14 Adding an H-dot

point		click


Lone Pair

The lone pair symbol is used for indicating a lone pair of electrons common in Lewis structure representations.

Figure 5-15 Lone pair symbol

Lone Pair

To draw a lone pair:

·	Point to where you want one end of the lone pair to be positioned.

·	Drag in the direction you want the end to be located and release the mouse button.

To quickly deposit a lone pair symbol in a horizontal orientation:

·	Click in a document window.

Figure 5-16 Adding a lone pair

point		drag


Radical

The radical symbol is used for indicating a single non-bonded electron.

Figure 5-17 Radical symbol

Radical Symbol
.To draw a radical:

·	Position the pointer next to an atom where you want the radical symbol to appear.

·	Click to draw the symbol.


Radical Cation and Radical Anion

The charge radical symbols are used for representing radicals that are charged.

Figure 5-18 Radical cation and radical anion symbols

Radical Cation		Radical Anion
.To draw a radical cation or radical anion symbol:

·	Position the pointer next to an atom where you want the symbol to appear.

·	Drag from the charge portion of the symbol to the radical portion of the symbol.

To quickly deposit a radical cation or radical anion symbol in a vertical orientation.

·	Click to deposit the symbol.


Chapter 5, Drawing Orbitals and Chemical Symbols - The Chemical Symbol Tool - Charges
Charges

The charge symbols are used for representing structures that are charged.

Figure 5-19 Negative and positive charge symbols

Circled Charges		Regular Charges
To draw a charge and associated it with a structure:

·	Click next to the atom to which you want the charge to correspond.

Notice that the number of hydrogens increases or decreases as appropriate for the addition of the charge symbol.

Figure 5-20 Adding a positive charge symbol

point		click


Chapter 5, Drawing Orbitals and Chemical Symbols - The Chemical Symbol Tool - Stereochemical Flags
Stereochemical Flags

To remove ambiguity for structures where there is more than one possible stereochemical interpretation, you can assign a special flag symbol to the structure.

Figure 5-22 The Racemic, Absolute and Relative symbols

To draw a flag:

·	Position the pointer next to the structure to which you want to assign the flag.

·	Click to deposit the symbol.

The font and size for stereochemical flags matches the default Atom Label size for the document.


Free Sites

Figure 5-23 Free Sites tool

To draw a free site symbol:

·	Position the pointer next to the atom whose free sites you want to establish.

·	Click to deposit the symbol.

·	Continue clicking to increment the free site count to the number you want.

You can also use the atom properties command to apply or increment the number of free sites.


Editing a Symbol

To rotate a Chemical Symbol:

·	Select the Chemical Symbol tool.

·	Hold down the Shift key and point at a Chemical Symbol.

A highlight box appears.

·	Drag the highlight box on the chemical symbol.

The symbols are rotated around the same end from which they were originally drawn. For instance, the radical cation symbol is rotated and resized from the charge. As you rotate symbols, the angle that one of the ends of a symbol makes with the X axis is shown in the Message area.

You can also rotate many of the symbols using a selection tool by dragging the Rotation handle on the Selection Rectangle. The charge and the radical symbols cannot be rotated. The rotation occurs around the center of the object as defined by the Selection rectangle. Equal rotations performed by a selection tool and the Chemical Symbols tool will result in a different final placement of the object rotated.


Chapter 6, Drawing Arrows, Arcs and Other Shapes - Overview
Overview

This chapter discusses four tools that you can use to add different kinds of shapes to your documents. These tools include the Arrow tool for drawing arrows, the Arc tool for drawing arcs, the Drawing Elements tool for drawing boxes, circles and brackets, and the Pen tool for drawing freehand shapes.

The Arrow, Arc and Drawing Elements tools each contain a palette from which you can choose from different types of that tool. Once you choose a tool from the palette, that tool can be used without choosing from the palette again.

To select a tool and use its default object:

·	Click the tool's icon to select it.

To choose a different object from the palette.

·	Point to the tool's icon and hold down the mouse button.

The palette appears.

·	Drag to select an object from the palette.

·	Release the mouse button over the object you want to select.

The new object becomes the default used for that tool whenever you select the tools icon from this point forward, until you make another selection from the palette.

The remainder of this chapter will step through each of the tools individually.


The Arrow Tool

The Arrow tool is used for adding arrows to show conversion of reactants to products as well as indicating electron flow (you can also use the Pen tool, discussed later in this chapter, to make customized arrows).

Figure 6-1 Arrow tool

Figure 6-2 Types of arrows in the Arrow Tool palette

A. Normal B. Hollow C. Retrosynthetic D. Bold E. Two-electron curved F. Dashed	G. Half-arrow above H. Single-electron curved I. Half-arrow below J. Resonance K. Equilibrium
More:

Drawing an Arrow

Editing an Arrow


Drawing an Arrow

·	Select the Arrow tool.

·	Point in the document where you want the end of the arrow to appear.

·	Drag to where you want the arrow head to be.


Editing an Arrow

To lengthen, shorten or rotate an arrow:

·	Select the Arrow tool.

·	Hold down the Shift key and point to the head of the arrow.

A highlight box appears over the head of the arrow.

·	Drag the arrowhead.

The arrow is resized and rotated relative to its end. As you drag, the change in length and the angle the arrowhead makes with the X axis appear in the Message area.

You can also resize and rotate an arrow using a selection tool by dragging the Resize or Rotation handle on the Selection rectangle. The Message area indicates the percentage enlarged or reduced when you drag the Resize handle and the number of degrees rotated when you drag the Rotation handle. The resize or rotation occurs around the center of the Selection rectangle. Equal rotation or resize operations performed by a selection tool and the Arrow tool will result in a different final placement of the object. You cannot change the aspect ratio of arrows.


The Drawing Elements Tool

The drawing elements tool provides a variety of shapes that an add to your drawing.

Figure 6-3 The Drawing Elements tool

Several Drawing Element types are available with different fill patterns: hollow (no fill pattern), gray and black.

Gray Drawing Element types appear with grayscale shading on color and grayscale monitors and print with grayscale shading from PostScript printers when the Color/Grayscale option is selected in the Print dialog box.

Related groups of Drawing Element types are discussed below. While you draw any of the drawing element types, the length and angle relative to the X axis appears in the Message area.

More:

Boxes

Circles and Ovals

Single Brackets

Paired Brackets

Lines

Daggers

Editing Drawing Elements


Boxes

Figure 6-4 Boxes

To draw a box:

·	Select a box tool.

·	Point where you want a corner of the box to be located.

·	Drag from one corner of the box diagonally to the opposite corner.


Circles and Ovals

Figure 6-5 Circles and ovals

To draw a circle or oval:

·	Select a circle or oval tool.

·	Point where you want the center of the circle to be located.

·	Drag outward from the center.

NOTE: to make other styles of circles, such as a dashed circle, you can use the pen tool with dashed style. See "Pen Tool" later in this chapter.


Single Brackets

To draw an single bracket:

·	Select a single bracket tool.

·	Point where you want the bracket to start.

·	Drag from one end of the bracket to the other end.

A single bracket can be drawn in any orientation.

Figure 6-6 Single brackets


Paired Brackets

To draw a paired bracket:

·	Select a paired bracket tool.

·	Point where you want a corner of the bracket to be located.

·	Drag from one corner of the box diagonally to the opposite corner.

Paired brackets can only be placed in a vertical orientation. Their position is defined by a rectangle or box.

Figure 6-7 Paired bracket


Lines

Lines drawn with the line tool differ in two significant ways from bonds drawn with the bond tools: they are not counted in chemical interpretation of the drawing, and they do not "drop out" when they cross one another.

To draw a line:

·	Select a line tool.

·	Point where you want the line to start.

·	Drag from one end of the line to the other end.

Figure 6-8 Dashed and solid lines


Daggers

i Elements:circles ;To draw a dagger:

·	Select a dagger tool.

·	Point where you want the symbol to be located.

·	Click to deposit the dagger.

Figure 6-9 Daggers

NOTE: Drawing elements, such as brackets, are not actually part of the structure they are drawn near, and are not selected if you double-click on a bond, atom or atom label with a selection tool. To group drawing elements with a structure, use the Group command in the Object menu.


Editing Drawing Elements

To resize or rotate a drawing element:

·	Select the Drawing Element tool.

·	Hold down the Shift key and point to an end or edge of a drawing element.

A highlight box appears.

·	Drag the object to the new size or orientation (not valid for boxes and closed brackets)

The drawing element is resized or rotated from the same point that it was originally drawn. For instance, a shadowed box is resized from the corner where the shaded edges meet. The length of the drawing element and the angle it makes with the X axis appears in the Message area. Boxes and paired brackets cannot be rotated.

NOTE: The size of the dagger symbol is proportional to the Atom Label font size specified in the Text Settings dialog box.

You can also resize and rotate many of the drawing elements using a selection tool by dragging the Resize or Rotation handle on the Selection rectangle. You cannot rotate Dagger symbols. The percentage enlarged or reduced when you drag the Resize handle and the number of degrees the object rotates when you drag the Rotation handle appears in the Message area. The resize or rotation occurs around the center defined by the Selection rectangle. Equal rotation or resize operations performed by a selection tool and the Drawing Elements tool will result in a different final placement of the object.

Distorting circles and ovals (Alt+dragging (or Command+dragging) the Resize handle) converts these objects into an equivalent closed curve. Distorting gray shaded circles and ovals converts these objects to solid filled curves where the fill color is the same as the color of the curve. You can also distort boxes and closed brackets. The remaining Drawing Element types cannot be distorted.

Closed brackets and boxes cannot be rotated in the usual sense; however, when a box or closed bracket is rotated along with object(s) within its borders, the area of the box or closed bracket increases to accommodate the rotation of the contained objects.


The Arc Tool

The Arc tool is used to draw arcs of different angles: 90, 120, 180, and 270 degrees

Figure 6-10 The Arc tool and palette

Arc tool		Arc types
NOTE: On a small monitor, such as on the SE/30, the Arc types described in this chapter are located in the Drawing Elements palette discussed earlier in this chapter.

More:

Drawing an Arc

Editing an Arc


Drawing an Arc

To draw an arc:

·	Select an arc tool.

·	Drag from the left edge of the arc to the clockwise end of the arc in a document window.

While you draw an arc, the length between the ends, and the angle the clockwise end makes with the X axis appears in the Message area.


Editing an Arc

To resize or rotate an arc using the Arc tool:

·	Select the Arc tool.

·	Hold down the Shift key and point to the clockwise end of the arc.

A highlight box appears.

·	Drag the clockwise end of the arc.

The arc is resized and rotated relative to the first end from which it was drawn. The distance between the ends of the arc and the angle the clockwise end makes with the X axis appears in the Message area.

You can also resize and rotate an arc using a selection tool by dragging the Resize or Rotation handle on the Selection rectangle. The Message area indicates the percentage enlarged or reduced when you drag the Resize handle and the number of degrees rotated when you drag the Rotation handle. The resize or rotation occurs around the center defined by the Selection rectangle. Equal rotation or resize operations performed by a selection tool and the Arc tool will result in a different final placement of the object. You cannot distort arcs.


The Pen tool

Using the Pen tool, you can draw shapes that are not provided in the arrow, orbital or drawing elements palettes. For instance, you can draw irregularly shaped arrows, curves depicting graphs or reaction coordinate diagrams, as well as any other irregularly-shaped solids.

Figure 6-11 The Pen tool

Below (Figure 6-12) are some examples of shapes that you can draw using the Pen tool.

Figure 6-12 Shapes drawn using the Pen tool

customized orbitals		unique arrows
curves and axes		geometric shapes
To select the Pen tool:

·	Click the Pen tool icon in the Tools palette.

Shortcut:

To toggle between a selection tool and the Pen tool:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh) or select a selection tool.

The last drawn curve and the selection tool are selected.

More:

Drawing Segments by Clicking

Drawing Bezier Curves by Dragging

Editing a Curve

Changing Shape

Adding a Segment

Deleting a Segment

Applying a Style


Drawing Segments by Clicking

The easiest way to draw shapes with the pen tool is to click repeatedly in an outline of the shape you want.

·	Select the Pen tool.

·	Point to where you want the beginning of the curve to appear.

·	Click to deposit an endpoint.

·	Move the cursor and click again to add a second endpoint. Continue until you have the curve you want.

·	Press the Escape key or click another tool.

Figure 6-13 Shapes drawn by clicking with the Pen tool

point and click		click several more times
NOTE: you might want to work in a magnified view so you can place the fewest strategically placed control points for obtaining the smoothest curve.


Drawing Bézier Curves by Dragging
Drawing Bezier Curves by Dragging

A second way to draw curves with the pen tool is to click and drag repeatedly to create curved segments.

·	Select the Pen tool.

·	Point to where you want the beginning of the curve to appear.

·	Click and drag in the direction of the curve.

·	Move the cursor to another position.

·	Hold down the mouse button and drag to create an arc.

·	Press the Escape key to get out of the drawing mode of the curve tool.

Once you hold down the mouse button, another endpoint is established. Dragging creates the curve portion of the segment.

Notice that an additional line appears tangentially to the curve. This is the direction line that you can use to control the "curviness" of the segment.

Figure 6-14 Creating a curve with the Pen tool

after creating the first segment, point and drag to create a curved segment		point and drag again to create another curved segment
There are two kinds of control points that define the curve of a Bezier curve: endpoint controls and direction controls. The curve will pass through each endpoint control in turn, and its path from one endpoint to the next is determined by the direction controls.


Editing a Curve

To select an existing curve:

·	Select the Pen tool.

·	Point at the center of the curve.

A highlight box will appear when you are positioned correctly.

·	Point at the center of the curve.

Figure 6-15 Selecting a curve with the Pen tool

point		click
A highlight box appears.

·	Click the highlight box to select the curve.

The components of the curve appears. The components of the curve are shown in Figure 6-16.

Figure 6-16 Appearance of handles on a selected curve


Changing Shape

The control points that appear as you draw a curve allow you to change the size and curve of a curve segment.

Each point that touches the curve is a endpoint handle. Dragging an endpoint handle increases or decreases the breadth of the curve.

Figure 6-17 Changing a curve by dragging an endpoint handle

point		drag
The lines that pierce each point are the direction lines for the segment. The direction line controls the direction of the curved portion of the segment.

Figure 6-18 Changing curve by dragging a direction handle

point		drag


Adding a Segment

To extend an existing curve:

·	Select the Pen tool, and click the existing curve you want to edit to select it.

The components of the curve appear.

Figure 6-19 Adding segments

point and click		point and drag
·	Point to the Endpoint handle of a curve until the cursor appears as a hand.

·	Ctrl+click (Windows) or Option+click (Macintosh) the endpoint.

The cursor now appears as a hand with a "+" sign inside, and note that the endpoint now appears has the components of a middle segment, i.e., it now has two tangent control lines. The Pen tool is in drawing mode.

·	Click and drag in the window to connect more segments to your curve.

To exit the drawing mode:

·	Press the escape key or click the Pen tool or any other tool, or double-click.

Figure 6-20 Using the Pen tool to draw reaction mechanism diagrams


Deleting a Segment

To delete a curve segment: (You should be in the edit mode of the Pen tool, i.e., the cursor should appear as a Crosshair.)

·	Ctrl+Shift+click (Windows) or Option+Shift+click (Macintosh) the control point where you want to delete a curve segment. (The cursor should appear as the Eraser tool before you click.)

You can also delete entire curves using a selection tool and the Eraser tool.


Applying a Style

To apply a style to a curve:

·	Select a curve using either the Pen tool or a selection tool.

·	From the Curves menu, choose a style.

All curves are drawn with the last curve styles chosen until you change the selections. Certain styles are mutually exclusive. For instance, if you choose Closed, you cannot also choose Arrow at Start.

To remove all styles from a curve:

·	From the Curves menu, choose Plain.

Figure 6-21 Shape with and without closed and filled style

normal		closed and filled


Chapter 7, Working with Selections - Overview
Overview

A large portion of the editing in ChemDraw is performed on objects that are selected. Selection can be performed with either the Lasso or the Marquee selection tools. With these tools, objects can be selected individually or as groups. Once objects are selected, you can duplicate, move, resize, rotate or delete them. This chapter describes these and other editing operations you can accomplish with the Lasso or Marquee selection tool.


Using the Selection Tool
Using a Selection Tool

You can use either the Lasso or the Marquee selection tool for all of your selection needs. These tools differ only in the default mode that is used for selecting: free hand for the Lasso and rectangular regions for the Marquee.

To transform one selection tool so that it behaves like the other:

•	Hold down the Ctrl key (Windows) or the Option key (Macintosh).

Figure 7-1 The Lasso and Marquee Selection Tools

Lasso		Marquee
·	Click either the Lasso or Marquee tool.

Whenever you select a selection tool, the last objects drawn are automatically selected.

 A selection is identifiable by the shimmering "Selection rectangle" that encloses the object.

Figure 7-2 A Selection rectangle

Shortcut:

To quickly switch to a selection tool from some other tool:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh).

A selection tool and the last drawn object are selected.

To switch from a selection tool to the last drawing tool used:

·	Press Ctrl+Alt+Tab (Windows) or Command+Tab (Macintosh).

More:

Selecting Objects by Clicking

Selecting Entire Structures

Selecting Objects with the Lasso

Selecting Objects with the Marquee

Adding to the Selection

Removing Objects from the Selection

Selecting All Objects

Deselecting All Objects

Deleting Objects

The Eraser Tool


Selecting Objects by Clicking

To select an object by clicking:

·	Select either the Lasso or the Marquee tool.

·	Point to an object in a document window.

A highlight box appears over the objects that will be selected when you click. If you point at a bond, the highlight box appears over the length of the bond.

·	Click a bond, an atom or other object.

The selected objects appear within the Selection Rectangle and the cursor changes to a hand.

Figure 7-3 Selecting a bond

point to a bond		click

Figure 7-4 Selecting an atom

point to an atom		click
NOTE: If the bond or other object is part of a group you can still select it as an individual object. For more details about grouping objects see "Grouping" later in this chapter.

Preferences Guide

Tolerance

The size of the highlight box (and how close you must get to an object to activate highlight boxes) is controlled by the measurement in the box labeled "Tolerance" in the Preferences dialog box. The standard setting for the Tolerance is 5 pixels. This means, for instance, that the highlight box appears on bonds if the pointer is located 5 pixels or less from any point on the bond.

To change the Tolerance:

·	From the File menu, choose Preferences.

·	Click the up or down Tolerance control arrow to increase or decrease the tolerance.

This change affects all documents.


Selecting Entire Structures

To select an entire chemical structure:

·	Double-click a bond or atom within the structure.

The entire chemical structure is selected. If the chemical structure or other object is part of a group, the entire group is selected.

Figure 7-5 Selecting by double-clicking

point		double click


Selecting Objects with the Lasso

You can use the Lasso tool to encircle irregular areas using a freehand selection mode.

To select objects using the Lasso:

·	Select the Lasso tool.

·	Press the mouse button while the pointer is not over any object.

·	Drag around a portion of a chemical structure or other object.

As you drag around the object(s), a line appears which defines the Selection area. Only bonds, structures or other objects that are entirely enclosed in the Selection area will be selected. The end points of the Lasso are automatically connected when you release the mouse button.

Figure 7-6 Selecting parts of a structure using the lasso

point		drag


Selecting Objects with the Marquee

.You can use the Marquee tool to select objects and structures within a rectangular area.

 To select objects using the Marquee:

·	Select the Marquee tool.

The pointer becomes a Marquee.

·	Drag diagonally across the chemical structure(s) or other object(s).

As you drag, a rectangle appears which defines the Selection area. Bonds and other objects are selected only if they are entirely within this area. The Marquee is useful for selecting several objects at once as long as they can be surrounded by a rectangle.

Figure 7-7 Selecting parts of a structure using the Marquee

point		drag


Adding to the Selection

To make multiple selections or add more objects to the selection:

·	Hold down the Shift key and select several other objects.

Objects can be added to the Selection by clicking, double-clicking or by using the Lasso or the Marquee.

Figure 7-8 Adding to a selection using the Marquee mode of a selection tool

point		drag over items to add to the selection


Removing Objects from the Selection

To remove an object from the selection:

·	Hold down the Shift key and select an object contained within the Selection rectangle by clicking, double-clicking, or Lassoing.

The object is removed from the selection.

NOTE: Objects may appear within the borders of the Selection rectangle, but not be selected. Only objects that are shimmering are selected.


Selecting All Objects

To select all objects within a document window:

·	From the Edit menu, choose Select All.


Deselecting All Objects

To deselect all selected objects:

·	Click in any empty area in a document window that is outside the Selection rectangle.

Alternatively:

·	Press the Escape key.

All selected objects are deselected. You can also deselect all selected objects by selecting a different tool or by selecting another object without holding down the Shift key.

Figure 7-9 Deselecting an object

point outside of the selection		click


Deleting Objects

You can delete selected objects using the Delete key, the Clear command, or the Eraser tool.

More:

Delete key

Clear Command


Delete key

To delete object(s) using the Delete key (or the Backspace key):

·	Select the object(s) you want to delete.

·	Press the Delete key.


Clear Command

To delete object(s) using the Clear command:

·	Select the object(s) you want to delete.

·	From the Edit menu, choose Clear.


The Eraser Tool

With the Eraser tool you can delete objects selectively. For instance, you can reduce the bond order of a multiple bond, or erase a single bond. Below are the general rules followed by the Eraser tool:

⇒ Clicking a labeled atom removes the label.

⇒ Clicking an unlabeled atom removes the atom and all adjacent bonds.

To select the Eraser tool:

·	Click the Eraser tool icon in the Tools palette.

Figure 7-10 The Eraser Tool

To erase a bond:

·	Click a single, double or triple bond.

The bond order is reduced by one.

Figure 7-11 Erasing one bond of a double bond

point		click (and move cursor away)

Figure 7-12 Clicking a single bond with the Eraser tool

point		click (and move cursor away)


Moving Objects

To move an object:

·	Select the object(s) using a selection tool.

·	Point within the border of the Selection rectangle.

·	Drag the object(s).

Figure 7-13 Moving a selected object

point		drag
To constrain the movement to the horizontal or vertical direction:

·	Alt+drag (Windows) or Command+drag (Macintosh) the selected object(s).

Figure 7-14 Moving and constraining a selected object

point		Alt + drag (or Command +drag)
To move selected objects a small distance using the Arrow keys available on many keyboards:

·	Press an arrow key while object(s) are selected.

The selected object(s) move 1 point (1/72 inch, 0.035 cm) in that arrow's direction.

To move in a larger increment, for example, to the right:

·	Press Ctrl+Right Arrow (Windows) or Option+Right Arrow (Macintosh)

The selected objects move 10 points (10/72 inch, 0.35 cm) in that arrow's direction. These small incremental movements are often useful for aligning objects.

NOTE: See Chapter 12, Working with Page Layout, for more information about aligning objects.

More:

Using the Clipboard

Moving Atoms


Using the Clipboard

To remove the objects contained in the Selection rectangle for later repositioning in the current document window, or for transferring to another ChemDraw document or other type of document:

·	Select the object(s) using a selection tool.

·	From the Edit menu, choose Cut.

The object is transferred to the Clipboard and deleted from a document window. You can transfer the copy on the Clipboard to another position in the same document, another ChemDraw document or a different type of document.

To paste a copy of the contents of the Clipboard into a document window.

·	Select a selection tool.

·	From the Edit menu, choose Paste.

You can also use Drag and Drop to move selections between ChemDraw documents. See "Drag and Drop" in Chapter 13, Sharing Information, for additional information.


Chapter 7, Working with Selections - Moving Objects - Moving Atoms
Moving Atoms

You can move the atoms within a chemical structure using a selection tool.

To move a single atom:

·	Point to an atom using a selection tool.

·	Drag the atom.

The bonds connected to the atom stretch as it is dragged.

To move multiple atoms:

·	Select only the bonds that have atoms on both ends that you want to move.

The unselected bonds that are attached to the selected atoms will be stretched.

Figure 7-15 Dragging a selection

select and point		drag
NOTE: You can also move atoms using the bond tool that was used to draw the atom.


Duplicating Objects

To duplicate objects with a selection tool:

·	Select a selection tool.

·	Select the object(s).

·	Ctrl+drag (Windows) or Option+drag (Macintosh) to create a copy and position it.

A copy of the selected objects is moved to the new position.

Figure 7-16 Duplicating a selection

Ctrl (or Option) + point		drag
To duplicate the selected objects and constrain the positioning of the copy to the same horizontal or vertical position as the original objects:

·	Select a selection tool.

·	Select the object(s).

·	Ctrl+Alt+drag (Windows) or Option+Command+drag (Macintosh) to create a copy and position it.

To place a copy of an object on the Clipboard:

·	Select the object(s) using a selection tool.

·	From the Edit menu, choose Copy.

A copy of the object is placed on the Clipboard. Using the Paste command, you can transfer the copy in the Clipboard to the current document, another ChemDraw document, or a different document type.


Rotating Objects

To rotate object(s):

·	Select the object(s) to rotate using a selection tool.

·	Drag the Rotation handle clockwise or counterclockwise.

The Rotation handle is located in the upper-right corner of the Selection rectangle:

Figure 7-17 Rotating a selection

point		drag downwards
As you rotate, the magnitude of the rotation around the center of the Selection rectangle appears in the Message area.

NOTE: Captions and atom labels that contain multiple colors will change to the foreground color when rotated. However, all colors contained in the captions are printed.

To rotate objects, but not atom labels:

·	Hold down the Ctrl key (Windows) or the Option key (Macintosh) and drag the Rotation handle.

To rotate the selected object(s) a specified number of degrees:

·	From the Object menu, choose Rotate.

·	Or, double-click the Rotation handle.

The Rotation dialog box appears.

·	Enter a positive whole number for a clockwise rotation or a negative whole number for counterclockwise rotation.

·	Click the Rotate button.

Objects are rotated around the center of the Selection rectangle.

To perform another rotation of exactly the same magnitude on any object in the document window, immediately after performing a rotation:

·	Select the other object(s) to rotate.

·	From the Edit menu, choose Repeat Rotate.


Reflecting Objects Through Planes

You can reflect structures through planes perpendicular to the X or Y axis using a selection tool. Used in conjunction with duplicating, you can create mirror images of chemical structures for representing racemic mixtures, and with a small amount of editing, other stereoisomers as well.

To reflect an object through a plane perpendicular to the Y axis:

·	Select the object(s) to reflect.

·	From the Object menu, choose Flip Vertical.

To reflect an object through a plane perpendicular to the X axis:

·	Select the object(s) to reflect.

·	From the Object menu, choose Flip Horizontal.

Atom labels and captions do not flip along with the object.

Figure 7-19 Reflecting an object horizontally by choosing Flip Horizontal

select and flip		result


Resizing Objects

To resize an object or collection of objects:

·	Select the object(s) to resize.

·	Drag the Resize handle.

The Resize handle is located in the lower right corner of the Selection rectangle.

Figure 7-20 Resize handle

As you resize the selected object(s), the percentage you have enlarged or reduced it from the original size is shown in the Message area.

Figure 7-21 Resizing a selection

point		drag
NOTE: If all objects in the document window are part of the selection you are resizing, a message appears after you resize that asks whether you want to change the document settings for that document. If you choose to do so, all subsequent bonds, atom labels and captions (depending on what is in the selection) will be drawn using these new settings.

More:

The Scale Dialog Box

Distorting a Selection


The Scale Dialog Box

You can also resize objects with the Scale command:

·	Select the object(s) to scale.

·	From the Object menu, choose Scale,

·	Or, double-click the Resize handle.

The Scale Dialog Box appears.

The first two options in the Scale dialog box are used to scale all selected objects so that the median selected bond has a specified length based on the following scale factor:

Figure 7-23 Scale factor equation

To scale bonds in the selected objects so that the Fixed Length indicated in the Drawing Settings dialog box is used as the new median bond length:

·	Select the top option/radio button.

The fixed length presently in the Drawing Settings dialog is shown in parentheses at the end of the line for this button.

·	Click the Scale button.

To scale the bonds to a new fixed length that you specify:

·	Select the middle option/radio button.

·	Type the new median bond length in the box to the right of the button.

The current median bond length for the selection is shown in the highlighted text box when the dialog box initially appears.

·	Click the Scale button.

To scale object(s) by a percentage:

·	Select the bottom option/radio button.

·	Type the percentage in the box to the right of the button.

·	Click the Scale button.

This last option is the only one available when the selection does not contain any atoms or bonds.


Distorting a Selection

.In most cases, when you resize an object, the aspect ratio of the object (the ratio of the object's height to its width) does not change. However, it is possible to change the aspect ratio (distort) of certain objects including chemical structures, circles, boxes, and ovals.

To distort an object in the horizontal or vertical direction:

·	Select the object and Alt+drag (Windows) or Command+drag (Macintosh) the Resize handle.

The Alt key (Windows) or Command key (Macintosh) modifies the resize operation so that you can distort objects along the X or Y axis.

·	Drag the Resize handle.

Figure 7-24 Distorting a selection

hold down the Alt key (or Command key) and point to the Resize Handle		drag upwards


Joining Objects

Use the Join command in the Object menu to fuse two chemical structures together. Once structures are joined they can be easily selected by double-clicking.

To join chemical structures along the length of a bond:

·	Position the structures that you want to join so that the bonds you want to join are nearly overlapping (within tolerance).

Objects to be joined must be positioned close enough to be within the Tolerance setting specified in the Drawing Settings dialog box. Otherwise, the Join command will be inactive.

·	Select the chemical structures to join.

·	From the Object menu, choose Join.

To join chemical structures at one atom to create a spiro-linkage:

·	Select both chemical structures.

·	Position the two chemical structures so that two atoms nearly overlap.

·	From the Object menu, choose Join.

NOTE: When you join two differently colored bonds or atom labels, the color of the frontmost object becomes the color of the resulting joined object. See Chapter 12, Working with Page Layout, for more information about front to back ordering of objects.

NOTE: When you join two atoms that are labeled, the frontmost atom label becomes the atom label of the resulting atom.

Figure 7-25 Fusing bonds

select bonds and choose the Join command		result (after deselecting)

Figure 7-26 Fusing atoms

select atoms and choose the Join command		result (after deselecting)

Preferences Guide

Tolerance

The maximum distance required between two atoms for joining to occur is controlled by the Tolerance setting in the Preferences dialog box. The standard setting for the Tolerance is 5 pixels. This means that two atoms will be joined if they are within 5 pixels of each other when you choose the Join command.

To change the Tolerance:

·	From the File menu, choose Preferences.

·	Adjust the number of pixels by clicking the up or down Tolerance spin button.

This change affects all documents.


Grouping

It is often convenient to group a number of objects drawn separately into a single group. All objects contained in a group can be selected by double-clicking with a selection tool. Objects within a group can be selected individually and manipulated while still remaining part of the group. Grouping does not lock the position or orientation of objects; grouping only creates an association between objects so they can be easily selected.

Grouped objects also maintain their relative positions when they are centered on the page, aligned or distributed.

Atoms and bonds making up a single chemical structure are always grouped. If you group part of a structure with other objects, the resulting group will contain the entire structure. If you add atoms or bonds to a grouped structure, the new atoms and bonds will be part of the group.

NOTE: Only one level of grouping is provided. For instance, if you create two grouped objects, group these groups and then ungroup them, you return to the individual objects — not the groups.

More:

Group

Ungroup


Group

 To group several objects:

·	Select the objects to group using a selection tool.

·	From the Object menu, choose Group.

To select a group:

·	Double-click an object within the group using a selection tool.

To select an individual object within a group:

·	Click the object using a selection tool.

The object is selected, not the group.

Figure 7-27 Clicking and double-clicking grouped brackets

clicking a Grouped Bracket		double-clicking a Grouped Bracket


Ungroup

To ungroup objects that are grouped:

·	Double-click a group using a selection tool.

·	From the Object menu, choose Ungroup.

All the objects previously grouped become individual objects.


Chapter 8, Advanced Drawing Techniques - Overview
Overview

This chapter discusses the advanced drawing features available in ChemDraw. These advanced features provide alternative ways to label atoms by using HotKeys and abbreviated forms of functional groups called "Nicknames." In addition, this chapter discusses advanced drawing techniques for adding bonds to specific characters in atom labels, expanding nicknames, and creating bonds whose attachment is not explicitly defined.


Using HotKeys to Label Atoms

Use ChemDraw HotKeys to quickly label atoms and apply atom properties. The file, "hotkeys.txt" (Windows) or "ChemDraw HotKeys" (Macintosh), located in your cd_items directory (Windows) or ChemDraw Folder (Macintosh), contains the HotKeys provided with ChemDraw. You can add or change HotKeys by editing the file in a text editor, such as Notepad, TeachText, or SimpleText. See the section "Creating HotKeys" to learn how.

There are several ways to use a HotKey to label an atom. Following are descriptions of each method.

More:

Method 1: labeling the last atom drawn

Method 2: labeling an atom at which you point

Method 3: Pointing at an atom using a selection tool

Method 4: Labeling atoms in a selection

Hard Coded HotKeys

Other HotKey Effects

Creating HotKeys


Method 1: labeling the last atom drawn

·	Draw a bond.

·	Press a HotKey.

The last atom drawn is labeled. Each time you draw a bond, the last atom drawn will be the HotKey atom.


Method 2: labeling an atom at which you point

·	Position the pointer over an atom.

A highlight box appears over the atom when you are using a bond tool or the Text tool.

·	Press a HotKey.

The label is added to the atom highlighted. If the label is a single element, such as "C", then the appropriate number of hydrogens are added to the label.

Figure 8-1 Labeling the α-atom using the HotKey "c"

point to an atom and press "c"		result (after moving cursor)


Method 3: Pointing at an atom using the Selection tool
Method 3: Pointing at an atom using a selection tool

·	Using a selection tool, position the pointer over an atom.

Highlight boxes appear over the bonds attached to the atom.

·	Press a HotKey.

Figure 8-2 Labeling the β-atom using the HotKey "c"

point to an atom and press "c"		result (after deselecting)


Method 4: Labeling atoms in a selection

·	Select several atoms using a selection tool.

·	Press a HotKey.

The atoms whose bonds are completely selected are labeled.

The element or label associated with the HotKey is added to the structure. Only atoms with all their bonds selected are labeled. No label will result if all bonds to the atom are not selected.

Figure 8-3 Labeling several atoms using the HotKey "c"

select bonds and press "c"		result (after deselecting)


Hard Coded HotKeys

Certain HotKeys provide other effects. These HotKeys are hard coded into ChemDraw and are not editable in the hotkeys.txt or ChemDraw HotKeys file. For instance, the HotKey "Enter " (or "Return") opens the atom label text box for the last atom drawn. See Table 8-1 for a list of hard coded HotKeys:

Table 8-1 Hardcoded HotKeys

HotKey	If you want to.
Enter (or Return) key	open the atom label text box.
space	remove an atom label.
/	when point to an atom, displays the Atom Properties dialog. If pointing to a bond, the Bond Properties dialog box is opened. See "Bond Properties" and "Atom Properties" in Chapter 9, Drawing Query Structures, for more information.
=	display the List Nickname dialog.
.	add an attachment point


Other HotKey Effects

Whenever new bonds are added to atoms that contain only a single element and hydrogen, the appropriate number of hydrogens will be added or removed from the label. This effect occurs for all labels regardless of their origin (HotKeys or the Text tool) if the atom label is set to Automatic justification. You can disable this effect if you choose Flush Left or another justification for the atom label.

For example, labeling an atom with CH2 followed by adding a bond will result in a change to CH for the labeled atom. If you remove the bond, the label will return to CH2.

Figure 8-4 Reducing the number of hydrogens when adding a bond

point		click


Creating HotKeys

To add or edit ChemDraw HotKeys::

Locate the file named "hotkeys.txt" in your cd_items directory or "ChemDraw HotKeys" in your ChemDraw Folder. Double-click its icon to open the file using Notepad, TeachText or the text editor of your choice. The file contains a simple list using the format shown in Figure 8-5. For example, the file in Figure 8-5 has the label COOH assigned to the "a" key, and the label CH3 assigned to the "c" key.

Any uppercase or lowercase alphanumeric key may be used as a HotKey with the exception of the hard coded HotKeys listed in Table 8-1. If a key is used more than once in the file, the one closer to the end of the file takes precedence.

Figure 8-5 Defining HotKeys in a text file

a COOH

b Br

c CH3

HotKeys defined in text file

To add a HotKey:

·	Add a new line and type the key you want to use

·	Type a space.

·	Type the label to associate with the key.

Keep in mind, HotKeys defined for single elements will always result in the adding of the appropriate number of hydrogens.

If you are creating a new HotKeys file you should check for the following.

·	Select a Text Only file format if you are using an application such as Microsoft Word.

·	Type "hotkeys.txt" (Windows) (or "ChemDraw HotKeys" (Macintosh) for the file name.

·	Select the cd_items directory (Windows) or the ChemDraw Folder (Macintosh) as the location to save the file.

·	Click the OK (or Save) button.


Nicknames

Nicknames allow you to create shorthand representations for functional groups that you can use in as an atom label or as part of a label (the key here is that Nicknames are chemically meaningful whereas any random text is not).

Commonly used Nicknames, such as Me, Et, Ph etc. are provided with ChemDraw 3.5 in the nickname.dat or ChemDraw Nicknames file located in your cd_items directory (Windows) or ChemDraw Folder (Macintosh). However, you can easily add to this list, or delete those that you don't use.

Figure 8-6 Using a Nickname to represent an ethyl group

Nickname Representation		Normal Representation
For added speed when using Nicknames, you can assign HotKeys to Nicknames. For example, in the Nicknames and HotKeys provided with ChemDraw 4.5, the HotKey, "4" labels an atom with "Ph" which is a Nickname representing a phenyl group. To learn more about HotKeys, see the previous section "ChemDraw HotKeys".

More:

Using Nicknames

Defining Nicknames

Viewing Nicknames

Deleting Nicknames


Using Nicknames

To use a Nickname to label an atom:

·	Create a structure.

·	Double-click an atom using a bond tool, or click an atom using the Text tool.

An atom label text box appears.

·	Type a Nickname label such as "Et".

The atom is labeled with the Nickname, however, the chemical significance of the expanded structure is retained.

To select a Nickname to apply to an atom using a HotKey:

·	Point to an atom.

·	Press the HotKey "="

The Nickname list appears.

·	Select a Nickname from the list.

·	Click the OK button.

To use a HotKey to label an atom with a Nickname:

·	Using one of the labeling methods discussed in the earlier section, "Using HotKeys", press a HotKey that defines a Nickname label. For instance press "4" to label an atom with "Ph", or press "=" to open the List Nicknames dialog box where you can select a Nickname to use.

NOTE: Nicknames are tokens. As such, a Nickname will not flip orientation when applied to the left side of a structure when using Automatic Justification. For example, in the absence of a defined Nickname, the label "OTHP" will appear as "PHTO" when applied to the left side of a structure. However, since the Nickname "THP" is defined, the label appears as "THPO". Also see "Automatic Justification" in Chapter 4, Captions and Atom Labels. To define your own Nicknames, you must have ChemDraw Pro.


Defining Nicknames

To define a new Nickname:

·	Create a structure containing the functional group you want to define as a Nickname.

·	Select the functional group.

There must be an atom that has some bonds selected and other bonds not selected indicating the connection point for the functional group. See the examples below.

NOTE: You can define Nicknames with either 1 or 2 connection points. However, the connection points must be single bonds.

NOTE: If stereochemistry is indicated in a structure that you are defining as a Nickname, the stereochemistry is retained.

·	From the Structure menu, choose Define Nickname.

The number of connection points are shown by bullets after the Formula. You can have only one or two connection points in a nickname.

·	Type a short name for the Nickname.

·	Click the Define button.

The Nickname is defined, and you can now label atoms using its name.

NOTE: If you use a name for your Nickname that is the same as an element name, you are alerted that the element will be replaced with the Nickname. For example using Ac for an acetyl group will replace the element Actinium. Further, the Check Structure and Analyze structure commands will recognize the label as an acetyl group rather than Actinium. Table 8-8 shows these conflicts. To return the proper interpretation of elements, choose List Nicknames from the file menu and delete the overriding Nickname definition.

Table 8-8 Default Nickname/Element name conflicts

Symbol	Nickname	Element
Ac	Acetyl	Actinium
Am	Amyl	Americium
Np	para-Nitrophenyl	Neptunium
Pr	Propyl	Praeseodymium
If, when defining a Nickname, the command Define Nicknames is dimmed, you have probably not allowed for a connection point or you have defined more than 2 connection points or the connection point is a double bond. In the example below, the functional group was drawn and the entire group selected. This is the incorrect way to define a Nickname since there is no atom that indicates a connection point. The Define Nicknames command is dimmed if you try to define a Nickname by this method. However, on the right, the sulfonamide group is attached to an unselected bond which defines a bond from sulfur as the connection point for the group. This is the correct way to define a Nickname.

Figure 8-8 Defining a Nickname with a single connection point

incorrect		correct
You must leave a bond unselected for each connection point. No more than two connection points can be defined in a nickname and no more than one attachment point on a single atom can be defined. Figure 8-10 shows some correct and incorrect definitions.

Figure 8-9 Defining Nicknames for groups that have two connection points

incorrect  definitions	correct definitions
The definition in Figure 8-11 was used for the amino acid, Ala. The unselected bond at each end of the structure indicates the connection points; Nitrogen on the left and Carbon on the right.

Figure 8-10 Further illustration of defining nicknames for groups with two connection points

connection points indicate by arrows

A peptide chain can be drawn by stringing these Nicknames together (Figure 8-12). Alternatively, you can string the Nicknames together in an atom label (below right), as long as there is a bond attached. Or, you can create a string of nicknames as a caption as long as formula style is applied.

Figure 8-11 Drawing a peptide chain by string together Nicknames

as atom labels		as caption in formula style


Viewing Nicknames

To view the list of defined Nicknames:

·	From the File menu , choose List Nicknames.

The Nickname List dialog box appears.

Alternatively, you can use the "=" HotKey discussed in previous sections.


Deleting Nicknames

To delete a Nickname.

·	Select the Nickname that you want to delete from the list.

·	Click the Delete button.

The Nickname is permanently removed.


Multi-center Bonds

The multi-center attachment feature allows you to draw, with chemical significance, polyhapto structures, e.g. ferrocene ((Cp)2Fe). The basic procedure for drawing structures with multi-center attachments is to draw a fragment of the structure, select it, and designate it as a fragment with multi-center attachment. You can then attach bonds to that multi-center node created to represent the selected atoms.

Figure 8-14 Nodes defined for multicenter attachment

ferrocene


Creating a Multi-Center Bond

To create a multicenter attachment point:

·	Select the structure whose center you want defined as a multi-center attachment point.

·	From the Structure menu, choose Add Multi-Center Attachment.

An asterisk is displayed with the fragment to show that it contains a multi-center node. This asterisk will not be visible once a bond is drawn to it.

NOTE: You can check that the multi-center attachment point is there by positioning the cursor over the attachment point using a structure drawing tool or a selection tool. The asterisk will appear in the highlight box.

Figure 8-15 Creating a multicenter attachment point

select		choose multi-center attachment
To draw a bond to a multi-center attachment point:

·	Select the Bond tool.

·	Point to the asterisk and either click or drag to create a bond.

Figure 8-16 Drawing and labeling a bond from a multi-center attachment

draw a bond		label
TIP: 1. To make the bond in ferrocene appear that it is coming from within the ring, double-click the wedged bond to make it come forward, or select the downward bond and choose Send to Back from the Object menu 2. Double-click on the cyclopentadienyl ring with a selection tool. Note that the entire structure, including the single bond, is selected. The Cp ring and the single bond are associated as one structural unit because the bond between them is recognized by ChemDraw.)

NOTE: For the best looking structure, you may want to toggle the Fixed Length command (by Command-L or Ctrl-L) to draw a longer than normal bond.

Once you draw a bond from the multi-center attachment point, the asterisk will disappear. However, you can check that the node is present by selecting a Bond tool or a selection tool and positioning the cursor over the attachment point. If you use a selection tool, only the attachment node will be highlighted. If you use the Bond tool, not only is the attachment node highlighted, but so are all of the atoms that it represents. This provides a way to check the definition of a pre-existing multi-center attachment point.

Figure 8-17 Pointing at an attachment point using different tools

pointing with Selection tool		pointing with Bond tool


Multi-attached labels

Multi-attached atom labels enable you to draw chemical structures more efficiently by allowing you to attach bond(s) anywhere along an atom label.

Figure 8-18 expanded (top) and compact form using multi-attached atom labels (bottom)

expanded structure

compact form with multi-attached atom labels

More

Adding Bonds to an Atom Label


Adding Bonds to an Atom Label

The basic procedure for drawing additional bonds to an atom labels is:

·	Draw your structure and attach any necessary atom label.

·	Select a Bond tool.

·	Position the cursor over the part of the atom label to which you want to attach additional bonds. (The selected part of the atom label will highlight accordingly.)

·	Click and drag from the atom label to draw your bond(s).

By dragging you can determine the orientation of the resulting bond. If you click to add a bond, there are several preferential orientations for the resulting bond as outlined below.

1. adding from the end of an atom label creates bonds that are preferentially horizontal.

2. adding from the middle of an atom label creates bonds that are preferentially vertical.

3. adding from the start of an atom label creates bonds that try to attain the chain angle setting in the Drawing Settings dialog box, otherwise the next best angle is used.

Figure 8-19 Adding a bond to an atom label

point to an atom in the label		click or drag to draw a bond


Expanding Labels

If you have drawn structures which contain defined nicknames or which contain long atom labels, you can have ChemDraw automatically redraw your structures in fully expanded form by choosing the Expand Label command from the Structure menu.

Figure 8-20 Annotated and expanded form of a structure

annotated form		expanded form
To expand atom labels:

·	Select a selection tool.

·	Select the label within a structure that you want to expand, or double-click the structure to expand all possible labels.

·	From the Structure menu, choose Expand Label.

Your structure is redrawn in its expanded form.

Figure 8-21 Expanding all expandable labels in a selected structure

Select and choose Expand label		Result (after deselecting)


Structure Clean Up

The Clean Up Structure command, found in the Structure menu is used to neaten molecules by regularizing bond lengths and angles (graphic objects such as arrows and aromatic circles are not affected). You can use Structure Clean Up to redraw structures that you may have drawn freehand or to neaten structures that you may have imported from another application.

Structure Clean Up will not necessarily create the best structure. Most structures have many "clean" forms, a problem that is particularly noticeable with straight-chain alkanes.

If only part of a structure is selected when you choose Clean Up Structure, the other atoms and bonds will not be affected.

NOTE: For some compounds, the Clean Up Structure command will produce a structure that extends beyond the bounds of the page. To view the entire structure, scale the structure or increase the size of the printed page. For more information, see “Resizing Objects” in Chapter 7, Working with Selections, or “Page Setup” in Chapter 12, Working with Page Layout.

The salient points to note about structure clean up are:

1) The goal is to regularize bond lengths and bond angles to make for a more aesthetic picture.

2) Optimum bond lengths are determined by the Fixed Length in the Drawing Settings dialog.

3) A given ring is redrawn only if all of its constituent bonds are selected.

4) Clean is not good about complicated ring systems, particularly ones containing: trans double bonds; triple bonds; several highly connected rings; large rings.

5) Multi-attached atom labels and variable attachment points cannot be cleaned (you will see no change).

6) Multi-center bonds cannot be cleaned (you will see no change).

7) Structures are rotated so that as many bonds as possible are at a multiple of 15 degrees.

8) Structure cleanup will preserve stereochemical meaning rather than the precise identity of specific wedged and hashed bonds.

To use Structure Clean Up:

·	Select the structure or part of the structure you want to clean up with a selection tool.

·	From the Structure menu, choose Clean Up Structure.

NOTE: Clean Up Structure is not smart about positioning molecules relative to other objects. Overlap may occur.

Example 8-22 Applying the Clean Up Structure command

Select structure and choose Clean Up Structure		Result (after deselecting)
Example 8-23 Preservation of stereochemistry after applying the Clean Up Structure command

Before		After


Checking Chemistry

The Analyze Structure command and the Check Structure command provide ways to check your structure for valence and label errors, and calculate information about the structure.

More:

Check Structure

Analyze Structure


Check Structure

You can check the chemistry of a selected structure, part of a structure or caption (in Formula style) using the Check Structure command. The algorithm for this command is based on normal valences and elements, and defined Nicknames.

To check the valences of all selected atoms in a structure:

·	Select a structure, part of a structure, or caption using a selection tool.

·	From the Structure menu, choose Check Structure

Each label in the structure is checked sequentially. When a label is incorrect, a message window appears. To continue checking the structure when a message appears:

·	Click the Ignore button.

To ignore all subsequent errors in a structure:

·	Click the Ignore All button.

To stop checking a structure when a message appears:

·	Click the Stop button.

The atom that is causing the problem is selected.

Preferences Guide

Check Structure when Copying to Clipboard or Exporting

To have ChemDraw perform a check structure analysis on any structure copied to the Clipboard:

·	From the File menu, choose Preferences.

·	Click the Check Structure When Copying to Clipboard or Exporting checkbox.

This change affects all documents.

Figure 8-24 Message box indicating the error found during the Check Structure command

Figure 8-25 Error found during the Check Structure command

Problem is Selected when you Click the Stop button.


Variable Attachment Positions

The Add Variable Attachment command, found in the Structure menu, allows you to draw different positional isomers of a compound using an abbreviated notation that retains chemical significance.

For example, you can draw explicitly the three isomers of dibromobenzene shown in Figure 8-28.

Figure 8-28 Explicit isomers of dibromobenzene

Or, through the use of variable attachment, you can express all three isomers as a single parent structure as shown in Figure 8-29.

Figure 8-29 Parent structure for representing isomers of dibromobenzene

The procedure for using variable attachment is similar to adding multi-center attachment.

·	Draw the structural fragment to which you want to assign a variable attachment node.

·	Select the fragment using a selection tool.

·	From the Structure menu, choose Add Variable Attachment.

An asterisk with a dot appears in the center of your fragment (Figure 8-30).

Figure 8-30 Structure with a variable attachment point

You can treat this attachment node just as you would treat the end of a normal bond.

·	Select a Bond tool.

·	Drag to draw bond.

NOTE: In the example below (Figure 8-31), fixed lengths was disabled (using the Command key (Macintosh) or Ctrl key (Windows), so a bond could be drawn extending further from the ring.

Figure 8-31 Drawing a bond from a variable attachment point node

point		Command (or Ctrl) drag
Once you draw a bond from the attachment node, the asterisk will disappear. However, you can check that the node is present by selecting a Bond tool or a selection tool and positioning the cursor over the attachment point. If you use a selection tool, only the attachment node will be highlighted. If you use the Bond tool, not only is the attachment node highlighted, but so are all of the atoms that it represents. This provides a way to check the definition of a pre-existing attachment node.

Figure 8-32 Pointing to a variable attachment point node

pointing with Selection tool		pointing with Bond tool


Analyze Structure

Analysis information

(ULTRA Only)Chemical Property Information

The Analyze command provides a quick way to generate the chemical formula, exact mass, molecular weight and elemental analysis for a structure, part of a structure or caption (in Formula style). In the ChemDraw Ultra version, you can calculate chemical properties such as LogP, MR data for a selected structure. Prior to the calculation, the Check Structure command is automatically performed.


Analysis Information

Using the Analysis dialog you can calculate the following types of information about a structure:

Name	Description
Formula:	the molecular formula showing the exact number of atoms of each element in the molecule.
Exact Mass:	the exact molecular mass of the structure, where atomic masses of each atom are based on the most common isotope for the element.
Molecular Weight:	the average molecular mass of the structure, where atomic masses are based on the average of all isotope masses for the element.
Elemental Analysis:	The percent by weight of each element in the structure.

To view information about a selected structure:

·	Select an entire structure, part of a structure or a caption (in Formula style).

·	From the Structure menu, choose Analyze Structure

The Analyze Structure dialog appears (If you have ChemDraw Ultra (Windows) you will see two tabs labelled Analysis and Properties. - click the Analysis tab to see the information discussed in this section).

If any of the valences or labels are not correct you are alerted with a message. See "Check Structure" in the last section for more information.

Figure 8-26 Analyze Structure dialog box for cyclohexane

To paste information about a structure as a caption:

·	Click the checkboxes for the information that you want to paste.

·	Click the Paste button.

The information appears as a multi-line caption below the structure. This information can be edited using the text tool as you would any caption.

NOTE: Charge, radicals and isotopes are accounted for when using the Analyze Structure command. See Appendix A, The Chemistry of ChemDraw, for more information.

Figure 8-27 Analysis of cyclohexane

Select the structure to analyze		Result after clicking the Paste button (and deselecting)


 Chemical Property Information

Calculation Method

In ChemDraw Ultra, an add-on, CS ChemProp Pro, give you the ability to calculate several physical and thermodynamic properties for a selected structure:

NOTE: Fragmentation methods and literature values are used for these calculations. Use the Report button to view references for the methods.

Name	Description
Log(P):	Prediction of the logarithm of the partition coefficient for n-octanol/water.
MR:	Prediction of the Molar Refraction index.
Henry's Law:	Prediction of the logarithm of Henry's law constant (unitless).
Boiling Point:	Prediction of the normal boiling point for the structure (reported in Kelvin at 1 atm).
Melting Point:	Prediction of the melting point for the structure (reported in Kelvin at 1 atm).
Critical Temperature:	Prediction of the temperature (reported in K) above which the gas form of the structure cannot be liquified, no matter the applied pressure (Tc).
Critical Pressure:	Prediction of the minimum pressure (reported as bars) that must be applied to liquefy the structure at the critical temperature (Pc).
Critical Volume:	Prediction of the volume occupied (reported in cm3/mol) at the compound's critical temperature and pressure (Vc).
Heat of Formation:	Prediction of the heat of formation, ΔHf, for the structure (reported in kJ/mol at 1 atm and 298.15K).
Gibbs Energy:	Prediction of the Gibbs free energy, ΔG, for the structure (reported in kJ/mol at 1 atm and 298.15K).
Windows: To calculate properties for a selected structure:

·	Select the structure to analyze.

·	Choose Analyze Structure from the Structure menu.

·	Click the Properties tab in the dialog box.

The properties for the selected structure appear in the dialog box..

To see more detail for the calculated properties:

·	Click the Report button.

A detailed list of information used for performing the calculation is shown in a text file within Notepad (Windows). This list includes additional properties as well as literature references used to perform the calculation.

Macintosh: To calculate properties for a selected structure:

·	Select the structure to analyze.

·	Choose Analyze Structure from the Structure menu.

·	Click the Properties button in the dialog box.

The results and a detailed list of information used for performing the calculation is shown in a text file within SimpleText (Macintosh). This list includes additional properties as well as literature references used to perform the calculation..


Calculation Method

You can change the method used to calculate these properties by choosing from the following options in the Calculation Method pop-up list. When you choose an option from the list, the calculated values in the dialog change to reflect your choice.

Method	Description
Best Method:	Default method showing all properties using the most reliable methods for calculation for the given structure.
Literature Values	Shows Log P and MR based on literature values rather than a calculation.
NOTE: Results for other fragmentation methods including the Broto, Crippern, Viswanadhan, Joback and Joback/Stein can be found in the report generated by the Report button


NMR Shift Information

NMR Shift Information

In ChemDraw Ultra, two add-ons, CS ChemHNMR Pro and CS ChemCNMR Pro, give you the ability to calculate proton NMR and Carbon-13 NMR chemical shift data for a selected structure.

Documentation for this add-on can be found in the electronic document “ChemNMR” on your ChemDraw Ultra (or ChemOffice Ultra) CD ROM.


Chapter 11, Working with Color - Overview
Overview

With the color capabilities of ChemDraw, you can create full color presentations of your chemical drawings to appear on your monitor, print on a color printer, or create 35mm slides using a film printer.

Most computers can display any of 16 million colors, but the number of colors that can appear at any one time may be limited by the particular monitor and display card installed in your computer.

In ChemDraw you can choose from a palette consisting of a Background Color, a Foreground Color, and up to twenty additional colors for any given drawing. A palette is stored in every document and Style Sheet/Stationery Pad. You can use Style Sheets/Stationery Pads to create a series of documents with the same color scheme. For more information on Style Sheets/Stationery Pads, see “Saving Customized Settings” in Chapter 1, ChemDraw Basics.

Using color you can:

·Color atoms and bonds in a mostly black-on-white drawing to highlight areas of interest.

·Color parts of a structure in a reaction scheme to indicate where starting materials end up in the products of a complicated mechanism.

·Use colored boxes and circles to highlight atoms or molecules.

·Create slides that are easier to view by using light objects on a dark background.

Color Menu

Changing the Color palette

Templates and Color

Saving Color Palette Settings


Color Menu

The Color menu contains the palette of colors that you can use to color objects and text in the document within the active window.

The Foreground color in the Color menu is the color used for all newly drawn objects. The Other colors in the Color menu can be used to change the color of objects that you select.

You can customize the Color menu using the Color Palette dialog box in the File menu. Colors can be added, or existing colors can be changed. Changing a color, for instance Other #2, changes all objects that are using the color.

NOTE: If you select an individual or grouped object that contains multiple colors, there will be a check mark next to each of the colors in the Color menu. The purpose of the check marks is to alert you that a change would affect more than one color.

More:

Coloring Objects

Coloring Text


Coloring Objects

Any object that you can select with a selection tool can also be colored.

To color an object:

·	Select the object in a document window using a selection tool.

·	From the Color menu, choose a color.

You can color individual bonds, part or all of a chemical structure, or objects such as boxes, curves, arrows, orbitals and reaction mechanism symbols.

The border of objects that are shaded or filled, such as white filled s-orbitals in the Orbitals palette, will be the same color as the shading or fill. The border of objects that are hollow, such as circles and hollow boxes in the Drawing Elements palette can be colored, but the inside of the object cannot.


Coloring Text

This section discusses coloring caption and atom label text.

More:

Captions

Atom Labels


Chapter 11, Working with Color - Coloring Text - Captions
Captions

Captions can be colored before or after they are typed, and can be colored as a whole or in part.

To color a caption:

·	Select the Text tool.

·	Click in the position where you want to place the caption.

·	From the Color menu, choose a color.

·	Type a caption.

·	Press Enter to close the Caption text box.

NOTE: Which key you use to close the Text box will depend on the current setting for the "Require Option+Return (or Ctrl+Enter) to Create New Line preference in the Preferences dialog box.

To color individual characters:

·	Select part of an existing caption using the Text tool.

·	From the Color menu, choose a color.

NOTE: Captions that contain multiple colors will change to the foreground color when rotated. However, all colors contained in the caption are printed.

To color several captions at once:

·	Select the captions using a selection tool.

·	From the Color menu, choose a color.


Chapter 11, Working with Color - Coloring Text - Atom Labels
Atom Labels

You can change the color of an atom label either before or after you type it.

To color an atom label before it has been typed:

·	Click an atom using the Text tool.

·	From the Color menu, choose a color.

·	Type an atom label.

·	Press Enter.

NOTE: Which key you use to close the Text box will depend on the current setting for the "Require Option+Return (or Ctrl + Enter) to Create New Line preference in the Preferences dialog box.

·	Select part of an existing atom label using the Text tool.

·	From the Color menu, choose a color.

To color several atom labels at once:

·	Select the atom labels using a selection tool.

·	From the Color menu, choose a color.

NOTE: Atom Labels that contain multiple colors will change to the foreground color when rotated. However, all colors contained in the atom label are printed.


Changing the Color palette

This section describes how to change the palette of colors available in the Color menu and the background color using the Color Palette dialog box in the File menu.

To change the palette of colors used in the current document:

·	From the File menu, choose a Color Palette.

The Color Palette dialog box appears.

The Background Color is used to fill the background of the current document in the active window. The Foreground Color is the default color used whenever you draw a new object. Other Colors are the colors available in the Color menu for changing the color of individual objects. The colors are represented in the same order that they appear in the Color menu. The Set button changes to reflect the color selected. For instance, if you select the second Other Color, the name of the buttons changes to Set Other Color #2. When you select either the foreground or background color, the button changes to Set Foreground Color, or Set Background Color.

To change a color in the color palette:

·	Click the color you want to change.

A highlight box appears around the color, indicating that it is selected, and the Set Color button changes to the number associated with the color. For instance Set Other Color #2.

·	Click the Set Color button or double-click the color.

The Color Wheel dialog box containing the Macintosh Color Wheel appears (in System 7.5, the Color Picker appears).

NOTE: For information about the Color Picker, see your System 7.5 help file.

The Color dialog box appears.

To specify a new color: (Windows)

·	Click a color box in the Basic Colors section or the Custom Colors section.

A highlighted border appears around the color you select. To change to this new color:

·	Click the OK button.

The color is changed to the new color and can be chosen from the Color menu of the active document window.

If, while in the Color dialog box, you do not find the color you want, you can create customized colors by doing the following:

·	Within the Color dialog box, click the Define Custom Colors button.

The Color dialog box expands.

The selected color appears in the left half of the Color/Solid box in the lower portion of the dialog box. You can change the hue, saturation, luminosity, and RGB components by changing the numbers in the boxes. You can also select a custom color by doing the following:

·	Click a color in the Color Refiner box to set the hue and saturation.

The pointer turns into a Crosshair when you click. You can also hold the mouse button down and drag to a different region to change the hue and saturation.

·	Next, click within the Luminosity box to set the brightness of the color.

When you have the color you want, click the Add button to add it to the Custom Colors.

To specify a new color: (Macintosh)

·	Click a color in the Color Wheel.

The selected color appears in the upper half of Highlight Color Square, located in the upper left corner of the dialog box. The hue, saturation, brightness, and RGB components are listed on the left for the color that you have chosen. You can adjust the color by changing values within these boxes, in addition to, or instead of choosing from the Color wheel. For more information about the Macintosh Color Wheel, refer to your System documentation.

·	Click the OK button.

The Color Wheel dialog box disappears and the newly selected color appears in the Color Palette dialog box replacing the color you originally clicked.

More:

Adding Colors

Removing Colors


Adding Colors

To add a new color to the Color menu:

·	Click the New Color button.

 The Color dialog box appears.

·	Click the color to add or create a customized color. Or, for the Macintosh, click a color in the Color Wheel.

The selected color appears in the upper half of Highlight Color Square, located in the upper left corner of the dialog box. The hue, saturation, brightness, and RGB components are listed on the left for the color that you have chosen. You can adjust the color by changing values within these boxes, as an alternate method from choosing from the Color wheel.

·	Click the OK button in the Color Wheel dialog box.

The Color wheel dialog box disappears and the new color is added to the list of Other Colors.


Removing Colors

To remove a color from the Color menu:

·	Click the color you want to remove.

A highlight box appears around the color.

·	Click the Remove Color button.

The color disappears from the list of other colors.

To have all the changes take effect in the current document:

·	Click the OK button in the Color Palette dialog box.

The Color Palette dialog box disappears. If you changed the background color, the background of the document is changed. If you changed the default foreground color, any object that was colored in the previous foreground color is now colored using the new foreground color. In addition, any new object you draw will also appear in the new foreground color. If you changed any of the other colors, objects previously drawn in those colors are changed to the new colors. If you removed a color, objects that were drawn in that color are changed to the Foreground color.

If you do not want any of the changes that you have made in the Color palette dialog box to take effect:

·	Click the Cancel button in the Color Palette dialog box.


Templates and Color

The background and foreground colors used in a template from the template pop-up palette are not used when the template is drawn in a document window. However, any other colors used in the template are added to the color palette of the current document if they are not already present. This is part of the autoscale feature.


Saving Color Palette Settings

 If you have customized the Color menu for a particular document that you know you will want to use again, you can save the Color Palette in a Style Sheet. The Color Palette is saved in addition to other document settings that you have made for the document such as Page Setup settings, Text settings, and Drawing settings. To learn more about saving settings in Style Sheets/Stationery Pads see "Saving Customized Settings" in Chapter 1, ChemDraw Basics.


What Are Query Structures?

Searching of chemical databases such as ChemFinder, DARC, or ISIS/Base is often most efficient when you specify properties for atoms and bonds in a query structure. Depending on the query structure you create, a more narrow or more broad search can be initiated. For instance, you might broaden a search by creating a query structure where you have applied bond properties indicating a bond as either double or single, or you might narrow a search by applying atom properties where a particular atom must have a charge of +3.

Because ChemDraw is not itself a chemical database application, the interpretation of query structures necessarily involves other programs. Not all databases support the same query properties. If you use a query structure containing properties not understood by a given database, you might get an error message from that database, or it might simply ignore the properties that it does not understand.

To use query structures for searching, you will likely be able to paste the query structure into a database's search window and initiate a search. Alternatively, you may need to save the structure in an appropriate file format and open the file in the database application.

A list of the query properties recognized by ChemDraw cam be found in Table 9-13, later in this chapter, including how they are interpreted by some other common database programs. Also see "Transferring Information to Other Applications" in Chapter 13, Sharing Information, or consult the documentation for your chemical database.

NOTE: It is possible to assign conflicting or nonsensical properties. For example, you can require that one of the atoms in benzene is not part of any ring, which is inherently impossible. The resolution of this sort of impossibility depends on the query system used, but generally will result in no hits being found.


Atom Properties

To assign properties to selected atom(s) in a structure:

·	Select an atom by clicking with a selection tool, or select multiple atoms by Shift+clicking.

·	From the Structure menu, choose Atom Properties or press the HotKey "/".

 NOTE: Alternatively, you can simply point to an atom and/or press the HotKey "/" to open the dialog box.

The Atom Properties dialog box appears.

·	Select the atom properties from the drop-down list boxes that you want associated with the selected atom(s).

·	Click the OK button.

Small characters appear adjacent to atoms that have associated atom properties.

Figure 9-2 Atom properties associated with a single atom and many atoms

one atom		many atoms
The character that appears depends on which query properties have been assigned. If more than one property is assigned, more than one character will appear adjacent to the atoms.

Table 9-1 Atom property indicators

Character	Query Property
*	Substituents: Free Sites (followed by the number of free sites)
U	Substituents: Up to (followed by the maximum number of substituents)
X	Substituents: Exactly (followed by the number of substituents)
H	Implicit Hydrogens
R	Ring Bond Count
S	Unsaturation
C	Reaction Change
T	Reaction Stereo
NOTE: The Abnormal Valence atom property does not provide any visual indicator. This allows you to use this property to disable Illegal Valence warnings for specific atoms without cluttering your structure diagram.

With the exception of the characters for the Substituents query property, the letters indicate only that a given property has been applied, and do not indicate the exact value of that property. To find the precise value of a query property setting:

·	Select the atom.

·	From the Structure menu, choose Atom Properties.

·	View the settings of the drop-down list boxes.

To remove atom properties from an atom:

·	Select the atom.

·	From the Structure menu, choose Atom Properties.

·	Click the Use Defaults button.

The atom properties are removed and the characters are no longer adjacent to the selected atom(s).

To remove specific atom properties:

·	Select the atom.

·	From the Structure menu, choose Atom Properties.

·	Select the default value for the atom property you want to (see the value labeled "default" in the Search Result descriptions below).

NOTE: You can view the atom properties for an atom using the HotKey "/". See "Using HotKeys to Label Atoms" in Chapter 8, Advanced Drawing Techniques.

The following are the atom properties that you can associate with an atom:

More:

Substituents

Implicit Hydrogens

Ring Bond Count

Unsaturation

Reaction Change

Reaction Stereo

Abnormal Valence


Substituents

The Substituents property specifies the number of substituents bonded to the selected atom(s). In ChemDraw, a substituent is defined as a non-hydrogen atom connected by a bond of any order.

In Figure 9-3 below, the carbonyl carbon (indicated by the arrow) in propanal has a substituent count of two: the beta carbon and the aldehyde oxygen. This is because the double bond to the aldehyde oxygen counts as only one substituent (even though it is a double bond, it is still just one bond), and hydrogens never count as substituents.

Figure 9-3 The carbonyl carbon in propanal has a substituent count of two

The substituent count atom property allows you to specify the number of bonds to an atom in the target structure, including bonds already drawn in the query structure.

Table 9-2 Substituent options

Value	Search Result
Unspecified	Default. Behavior is determined by the target databases. Some databases (including ISIS) will find compounds with any substitution at this atom; some databases (including DARC) will find only compounds with substitution exactly as drawn.
Free Sites	Find compounds in which the selected atom(s) may contain a range of substituents up to the number specified in the spin control plus the number of bonds as drawn. A value of zero is equivalent to saying that the substituent count must be as drawn. You can also use the Free Site symbol in the Chemical Symbol palette to apply and increment free sites. See Chapter 5, Orbitals and Chemical Symbols for more information.
Up to	Find compounds in which the selected atom(s) may contain a range of substituents up to the number specified in the spin control.
Exactly	Finds compounds in which the selected atom(s) contains the exact number of substituents as specified in the spin control, up to 15 substituents.


Implicit Hydrogens

The Implicit Hydrogens property specifies whether additional, implicit hydrogens may be attached to the selected atom(s). If implicit hydrogens are disallowed, all valences to that atom must be filled by bonds to non-hydrogen atoms.

Table 9-3 Implicit Hydrogens options

Value	Search Result
Not allowed	Finds compounds with no additional hydrogens attached to the selected atom(s).
Allowed	Default. Finds compounds regardless of whether hydrogens are attached to the selected atom(s).


Ring Bond Count

The Ring Bond Count specifies the number of bonds attached to an atom that are part of rings of any size. For simple cases, this also implies the maximum number of rings in which an atom can reside.

Table 9-4 Ring Bond Count options

Value	Search Result
Any	Default. Finds compounds in which the selected atom(s) can be a member of any type of ring, or a member of no ring at all.
No ring bonds	Finds compounds in which the selected atom(s) is acyclic.
As drawn	Finds compounds in which the selected atom(s) resides in the same type and number of ring(s) as drawn.
Simple ring	Finds compounds in which the selected atom(s) is a member of only one ring (the atom has two ring bonds).
Fusion	Finds compounds in which the selected atom(s) lies at ring fusions (the atom has three ring bonds).
Spiro or higher	Finds compounds in which the selected atom(s) is a member of a spiro or higher linkage (the atom has four or more ring bonds).


Unsaturation

The Unsaturation property specifies whether a multiple bond is attached to the selected atom(s).

Table 9-5 Unsaturation options

Value	Search Result
Unspecified	Default. Finds compounds regardless of whether a multiple bond is attached to the selected atom(s).
Must be absent	Finds compounds that do not have a multiple bond attached to the selected atom(s).
Must be present	Finds compounds that have at least one multiple bond (double, triple or aromatic) attached to the selected atom(s).


Reaction Change

The Reaction Change property specifies whether a change occurs at selected atom(s) after a reaction. This property is only meaningful when searching a database containing chemical reactions.

Table 9-6 Reaction Change options

Value	Search Result
May be anything	Default. Finds all compounds regardless of any change to selected atom(s) after a reaction.
Must be as specified	Finds all compounds that are changed at the selected atom(s) after a reaction as drawn.


Reaction Stereo

The Reaction Stereo property specifies that the selected atom(s) are stereocenters in a reaction. This property is only meaningful when searching a database containing chemical reactions.

Table 9-7 Reaction Stereo options

Value	Search Result
Any	Default. Finds all compounds regardless of the stereochemistry at the selected atom(s).
Inversion	Finds compounds whose the selected atom(s) has an inverted stereo configuration after a reaction.
Retention	Finds compounds whose selected atom(s) has an unchanged stereo configuration after a reaction.


Abnormal Valence

The Abnormal Valence property specifies whether selected atom(s) can have a valence other than normal. "Normal" valences for each element are defined in the Isotopes Table (Macintosh) or isotopes.txt file (Windows).

Table 9-8 Abnormal Valence Options

Value	Search Result
Not allowed	Default. Finds compounds where the selected atom(s) only has valences that are normal for that element. If necessary, hydrogen atoms are automatically added to or removed from the atom before transferring it to the chemical database. If the Check Structure When Copying to Clipboard or Exporting preference is turned on, an error message will warn of abnormal valences.
Allowed	Finds compounds with the specific valence drawn.
NOTE: If Abnormal Valence is Allowed, any Invalid Valence messages for those atoms will be ignored automatically by the Analyze Structure and Check Structure commands.


Bond Properties

To associate bond properties to selected bond(s) in a structure:

·	Select a bond using a selection tool, or Shift+click to select multiple bonds.

·	From the Structure menu, choose Bond Properties.

NOTE: Alternatively, you can simply point to a bond and or press the HotKey "/" to open the dialog box.

The Bond Properties dialog box appears.

·	Select the bond properties you want from the various drop-down list boxes.

·	Click the OK button.

Textual descriptors appear adjacent to bonds that have associated bond properties.

Figure 9-5 Bond properties associated with a single bond and many bonds

one bond		many bonds
The descriptor that appears depends on which query properties have been assigned. If more than one property is assigned, more than one descriptor will appear adjacent to the atoms.

Table 9-9 Bond property indicators

Descriptor	Query Property
Any	Bond Type: Any
S/D	Bond Type: S/D
D/A	Bond Type: D/A
S/A	Bond Type: S/A
Rng	Topology: Ring
Chn	Topology: Chain
Rxn	Reaction Center
The descriptor for the Reaction Center query property indicates only that this property has been applied, and does not indicate the exact value of that property. To find the precise value of a query property setting:

·	Select the bond.

·	From the Structure menu, choose Bond Properties.

·	View the settings of the drop-down list boxes.

To remove all bond properties from selected bond(s):

·	Select the bond(s).

·	From the Structure menu, choose Bond Properties.

·	Click the Use Defaults button.

The bond properties are removed and the indicators are no longer adjacent to the selected bond(s).

To remove specific bond properties:

·	Select the bond.

·	From the Structure menu, choose Bond Properties.

·	Select the default value for the bond property you want to remove (see the value labeled "default" in the Search Result descriptions below).

The following describes the bond properties that you can associate with a bond(s):

More:

Bond Type

Topology

Reaction Center


Bond Type

This property specifies the bond type of the selected bond(s). The first portion of the pop-up menu changes the selected bond(s) to the type chosen. The remainder of the choices specify more complex query bond types.

The default bond type corresponds to the current type of the bond (single, double, etc.) as drawn.

Table 9-10 Bond Type options

Value	Search Result
Single... Dative	Finds compounds with the bond type you select for the selected bond(s).
Double or Double Bold	Finds compounds whose selected bond(s) is double.
Double Either	Finds compounds whose selected bond(s) is double bonds and have either cis/trans stereochemical configuration.
Aromatic	Finds compounds whose selected bond(s) is aromatic.
Tautomeric	Finds compounds whose selected bond(s) is tautomeric.
Triple	Finds compounds whose selected bond(s) is triple.
Any	Finds compounds regardless of the bond type of the selected bond(s).
S/D	Finds compounds whose selected bond(s) is single or double.
D/A	Finds compounds whose selected bond(s) is double or aromatic.
S/A	Finds compounds whose selected bond(s) is single or aromatic.
NOTE: Not all bond types are supported in all file formats. When an unsupported bond type is saved to a given file format, it is converted to the closest equivalent that is supported.


Topology

The Topology property specifies the ring environment of the selected bond(s).

Table 9-11 Topology options

Value	Search Result
Unspecified	Default. Finds compounds regardless of environment.
Ring	Finds compounds where the selected bond(s) is part of a ring.
Chain	Finds compounds where the selected bond(s) is part of a chain (and is specifically not part of a ring).


Reaction Center

The Reaction Center property specifies that the selected bond is affected in a reaction. This property is only meaningful when searching a database containing chemical reactions.

Table 9-12 Reaction Center options

Value	Search Result
Unspecified	Default. Finds compounds regardless of its being a reaction center.
Center	Finds compounds where the selected bond(s) is affected by a reaction, but the type of change is unspecified.
Make/Break	Finds compounds where the selected bond(s) is either broken or created in a reaction.
Change	Finds compounds where the bond order of the selected bond(s) changes in a reaction.
Make&Change	Finds compounds where the selected bond(s) is either formed or broken, and where its type changes in a reaction.
Not Center	Finds compounds where the selected bond(s)  is notthat may be changed during the reaction but are not the reaction center.
Not Modified	Finds compounds where the selected bond(s) is not modified in a reaction.


Generic Nicknames

Generic nicknames are nicknames that represent a class of elements or structural moieties. For example, "M" can be a generic nickname for all metals, "X" can represent halides, and "Ary" can represent an aromatic substructure. If you are using a query system that recognizes generic nicknames, you can use these nicknames in drawing your query in ChemDraw.

Generic nicknames, like other nicknames, can also be assigned HotKeys. For information on assigning a HotKey to a nickname, see "Creating HotKeys" in Chapter 8, Advanced Drawing Techniques. You cannot, however, define the meaning of a generic nickname within ChemDraw because generic nicknames represent multiple (and perhaps an infinite number of) substituents. Generic nicknames have meaning only in the context of the search system you are using.

The generic nicknames recognized as chemically meaningful by ChemDraw are listed in "Generic Nicknames" located in the ChemDraw Folder (Macintosh) or in "generics.txt" located in your cd_items directory (Windows). These files are text files similar to the HotKeys text files. To edit the generic nickname files, use a text editor such as Notepad to open the files, make your changes, and save your changes.

To label an atomic position with a generic nickname, use the same procedures as labeling an atom:

·	Open a text box on an atom position by clicking with the Text tool, or double-click on an atom position with a Bond tool.

·	Type the generic nickname you want.

·	Press Return or click outside the text box.

NOTE: You cannot perform "Analyze Structure" or "Check Structure" on a structure with a generic nickname because, by definition, the structure contain variable substituents. If you do perform "Analyze Structure" or "Check Structure," the generic nicknames will be ignored and ChemDraw will report the chemical formula, mass, etc., as if the atom label containing the generic nickname were not selected.

Figure 9-7 Using a generic nickname to specify X as any halogen.


Element Lists

The element list allows you to define your search query more concisely. By labeling an atom position as a list of elements you specify that one of these elements must match in the structure for which you are searching. The elements in the element list must be separated by commas, but the brackets are optional. It is also optional to have a space after each comma.

Figure 9-8 An example of an element list

NOTE: An element list may contain only atomic elements, plus deuterium and tritium.

To create an element list:

·	Open an atom label text box.

·	Type an open bracket ("[") followed by a list of elements separated by commas ("Cl, Br, I"), followed by a close bracket ("]").

Figure 9-9 Creating an element list

type a list enclosed in brackets		close the text box

Figure 9-10 Creating a query structure to find compounds matching the following criteria:

a)	non-oxygen chalcogenide bonded to another atom;

b)	not necessarily carbon (a generic nickname);

c)	the bond type between the chalcogenide and the other atom to be a single or double bond.

The "A" label denotes that the atom may match any atom except hydrogen. The mark near the bond indicates that the bond has special properties; in this case, in the Bond Properties dialog, you specified that the bond type must be single or double, S/D. Finally, by entering "S,Se,Te" enclosed in brackets, you specified that one of these elements must match in the target structures.


Element Not-Lists

The element not-list is similar to an element list, but where an element list requires that one of the elements in the list matches the target structure, a not-list requires that the elements do not match. The elements in the element not-list must be separated by commas, but the brackets are optional. It is also optional to have a space after each comma. The word NOT must be in all-caps and must be followed by a space. Alternatively, the word NOT may be replaced with a minus sign.

Figure 9-11 Examples of element not-lists

NOTE: An element not-list may contain only atomic elements, plus deuterium and tritium.

To create an element not-list:

·	Open an atom label text box.

·	Type an open bracket, the word NOT, and a space ("[NOT ") followed by a list of elements separated by commas ("Cl, Br, I"), followed by a close bracket ("]").


Alternative Groups

The Alternative Group feature allows you to submit to your query system a search query that contains variable functional groups or substructures. Instead of submitting multiple queries on structures which share a common substructure, you can submit a single query with the parent structure. The parent structure would have attachment points to a list of alternative groups which you can define.

Alternative groups are also sometimes called R-Groups, S-Groups, G-Groups, or Generic Groups.

Figure 9-12 Defining an alternative group for the variable portion of the structure

More:

Defining an Alternative Group


Defining an Alternative Group

Figure 9-13 Alternative Group tool

·	Select the Alternative Group Tool.

·	Click and drag in the ChemDraw window to create an area large enough for you to draw your alternative groups.

Figure 9-14 Creating an Alternative Group box

point		drag
The Alternative Group Title box is automatically selected.

·	Type a title, such as R1, in the Alternative Group Title Box.

Figure 9-15 Creating an Alternative Group title

title box after dragging		type
·	Draw your substructure fragments in the Alternative Group Box.

Figure 9-16 Defining substructures

draw structures

Next, you need to specify where your substructure fragments should be bonded to your parent structure at the Alternative Group Label. To label the attachment points, use the Attachment Point tool.

Attachement Point Tool


Attachment Point tool

Figure 9-17 Attachment Point tool

·	Select the Attachment Point Tool.

·	Click on the substructure fragments where you want to place the attachment point. Or, you can use the HotKey ".".

An attachment point symbol appears where you click.

·	Repeat for all fragments.

Figure 9-18 Assigning an attachment point to one fragment

point		click

Figure 9-19 Alternative group fragments with attachment points

repeat for each attachment point
NOTE: The Attachment Points on your fragments are numbered (You will see these numbers on your screen only if you have "Show Attachment Rank Indicators" selected in the Preferences dialog box). These numbers correspond to the Bond Rank number on your parent structure, and together they indicate how the structure fragments bond to the parent structure. For each fragment, the attachment point combined with the bond with the same bond rank number make up one bond.

Figure 9-20 Numbering of attachment points

When you create a parent compound containing the alternative group that you have defined, a attachment point symbol appears next to the label. The attachment point number matches those found in the definition.

Figure 9-21 Parent compound and alternative group definition

Parent compound with alternative group definition		close up of parent compound
NOTE: The completed query can be saved as an F1 Query file. The fragments that are not inside the Alternative Group Box will be interpreted as G0 in the F1 Query file. If the Alternative Group Labels are not G1, G2, G3, etc., they will be renamed when they are written out in the F1 Query format.


Multiple Attachment Points

Having well-defined multiple attachment points on your structure fragments allows you to perform searches for specific materials. This type of search is especially useful if you are searching for conformationally similar structures. Suppose you want to find the two compounds below:

Figure 9-22 Targeted compounds

However, you are not interested in the two compounds below:

Figure 9-23 Undesired compounds

By specifying the attachment points order, you can exclude the unwanted hits. The parent structure below will satisfy the necessary requirements.

·	Draw the parent structure shown below.

Figure 9-24 Parent Structure prototype

·	Create an Alternative Group Box labeled "R1".

·	Draw the structure fragments and label them with attachment points.

Once the alternative group definition is complete, the attachment point symbols will appear in the parent compound.

Figure 9-25 Complete alternative group definition and a parent

alternative group definition		parent structure
By clearly numbering your attachment points, you have unambiguously specified that the methyl group must be adjacent to the amine group. Thus, the conformers that you are not of interest are excluded.

Attachment point numbering

The numbering of the attachment points is related to the front to back order of the attachment points. To set the order of the attachment points, click the ends of the bonds in order. The last point clicked will have the highest number.

To change the ordering of the attachment points:

·	Click the attachment points again with the Attachment Point tool.

·	Or, select an attachment point with a selection tool, and select Bring to Front or Send To Back in the Object menu.

The attachment point numbers are highest in the front.

Having numbered attachment points is especially useful when you want to specify precisely how you want the structure fragments to be connected to your parent structure as discussed in the last section on multiple attachment points.

Preferences Guide

Show Attachment Rank Indicators

Sometimes — particularly in publication-quality drawings — the numbering of attachment points is implicit and the numbered attachment rank indicators are superfluous. To hide the attachment rank indicators and remove the numbers from the attachment points:

·	From the File menu, choose Preferences.

·	Deselect the Show Attachment Rank Indicators checkbox.

Figure 9-26 An alternative group definition and a parent structure with attachment rank indicators hidden.

This change affects all documents.


Anonymous Alternative Groups

An anonymous alternative group is a cross between an element list and an alternative group. Where element lists are restricted to single elements only, anonymous alternative groups can contain any structure that can be represented in a textual form. Nicknames and generic nicknames are allowed in anonymous alternative groups. Anonymous alternative groups are a "shortcut" notation for regular alternative groups, eliminating the need to specify a name such as "R1" (hence, anonymous).

As with element lists, the anonymous alternative group allows you to define your search query more concisely. By labeling an atom position as a list of substructures you specify that one of these substructures must match in the structure for which you are searching. The items in the anonymous alternative group must be separated by commas, but the brackets are optional. It is also optional to have a space after each comma.

Figure 9-27 Some examples of anonymous alternative groups

The procedure for creating anonymous alternative groups is similar to creating element lists:

·	Open an atom label text box.

·	Type an open bracket ("[") followed by a list of elements, fragments, nicknames, or generic nicknames separated by commas, followed by a close bracket ("]").


Reaction Mapping

Preferences Guide -Automatic Mapping

Preference Guide - Always Display and Print

To assign atom to atom mapping for creating records for a reaction database, and for creating queries for searching a reaction database you can use the Map Reaction Atoms command for automatic mapping, and the Reaction Atom-Atom Map tool for manual mapping. Reactions must have only one step in order to be mapped properly. Multi-step reactions are not supported at this time.

Figure 11-1 Reaction Atom-Atom Map tool

During either type of mapping process, the mapping algorithm perceives and assigns a reaction center for the reactants and products.

Once a reaction map is established, pointing to an atom in one structure (when the Reaction Atom-Atom Map tool is selected) will automatically highlight the mapped atom in the other structure.


Automatic Mapping

To automatically create a reaction map.

•	Draw the reaction you want to map.

Figure 11-2 Reaction to Mapped

·	Select the reactants and products in the reaction using one of the selection tools.

Figure 11-3 Select structures to map

·	Choose Map Reaction Atoms from the Structure menu.

Figure 11-4 Resulting mapping

Numeric symbols appear on each reactant and product when the mapping is complete (and the Reaction Atom-Atom Map tool is automatically selected). The numbers that match between the reactant(s) and product(s) reflect the atom mapping established by the Map Reaction Atoms command. In addition, the symbol “Rxn” appears next to the bond(s) in the reactant and product that are perceived by the algorithm as being modified by the reaction. These symbols are bond properties that are automatically applied (see Chapter 8, Bond Properties, for information about the Reaction Center bond property).


Manual Mapping

In situations that require manual mapping of atoms, you can use the Reaction Atom-Atom Map tool. This might be necessary when the automatic mapping is applied to complicated reactions. In these cases you can manually readjust the reaction mapping.

Below is an example showing the use of the Reaction Atom-Atom Map tool to alter the mapping produced by the Map Reaction Atoms command.

Figure 11-5 Automatic mapping produced for a type of Cope Rearrangement

To use the Reaction Atom-Atom Map tool to supplement the automatic mapping:

•	Click the Reaction Atom-Atom Map tool in the Tools palette.

•	Point to the atom in the reactant whose mapping you want to establish. In this example, you would point to the acyclic carbon adjacent to the ether oxygen.

•	Drag from the Reactant atom to the corresponding product atom.

Figure 11-6 Manually mapping the "OH"

You can continue to set or change the mapping for other atoms in the reaction if necessary until you get exactly the mapping you want. For this example additional manual mapping is not necessary.

Figure 11-7 Atoms after Manual Mapping

You can continue to change the mapping for other atoms in the reaction if necessary until you get exactly the mapping you want. For this example additional manual mapping is not necessary.


Preferences Guide

Automatic Mapping

Deselect this option in the Preferences dialog box if you want to suppress automatic re-mapping of atoms other than your target atom when performing manual mapping with the Reaction Atom-Atom Map tool.


Clear Mapping

To clear all reaction mapping:

·	Select the structures whose mapping you want to remove.

·	Choose Clear Reaction Maps from the Structure menu


Export Reaction Map

Reaction mapping and reaction center perception information are stored in the native ChemDraw 4.5 file format (*.cdx) for reopening in ChemDraw as well as the ISIS Reaction file format for transfer to other applications that read atom mapping, such as ChemFinder and ISIS/Base. You can also copy mapped reactions via the Clipboard to these same applications.


Preferences Guide

Always Display and Print Atom Mapping

Select this option in the Preferences dialog box if you always want the symbols to appear (and print) on the atoms when reaction mapping has been performed. Deselecting this option changes the display so the symbols are shown only when you select the Reaction Atom-Atom Map tool.

When this option is deselected, atom mapping symbols will not print, even through a reaction map has been created.


Export Compatibility

Since query properties are only useful in the context of a chemical database, it is necessary to transfer your structures from ChemDraw into your search system. Unfortunately, not all file formats support the same query properties, and not all chemical databases support the same file formats. Consult the documentation for your database to see which file formats is supports.

Table 9-13 is a list of the query properties that ChemDraw writes to ISIS (SKC, TGF, and Clipboard) and DARC (F1, F1-Query, and Clipboard) file formats. All query properties are written to the ChemDraw 4.5 (CDX) file format. CDX is the preferred format to use when you want to retain all query properties in a drawing, but might not be compatible with your database system.

Table 9-13 Exported query properties

		ISIS	DARC F1-Query	Mol	Rxn

ATOM PROPERTIES

Substituents

	Unspecified
	Free Sites	a		a	a
	Up to		b	aa	aa
	Exactly	• c		• c	• c
Implicit Hydrogens

	Not allowed
	Allowed
Ring Bond Count

	Any
	Any
	No ring bonds
	As drawn
	Simple ring
	Fusion
	Spiro or higher
Unsaturation

	Unspecified
	Must be absent
	Must be present
Reaction Change

	May be anything
	Must be as specified

Reaction Stereo

	Any
	Inversion
	Retention
Abnormal Valence

	Not Allowed
	Allowed
		ISIS	DARC F1-Query	Mol	Rxn

BOND PROPERTIES

Bond Type

	Single
	Dashed		d
	Hashed	d	d	d	d
	Wedged Hashed
	Bold		e	e	e
	Wedged
	Wavy		• f
	Hollow Wedged	e	e	e	e
	Dative	g	g	g	g
	Double	• h		h	h
	Double Either
	Double Bold	i	i	i	i
	Aromatic		• j
	Aromatic		• j
	Tautomeric	k	k	k	k
	Triple
	Any		• l
	S/D
	D/A
	S/A

Topology

	Unspecified
	Ring
	Chain
Reaction Center

	Unspecified
	Unspecified
	Center
	Make/Break
	Change
	Make&Change
	Not Center
	ISIS	DARC F1-Query	Mol	Rxn

OTHER QUERY ATTRIBUTES

Generic Nicknames	• m	• n
Element Lists	• o		• o	• o
Element Not-Lists	• o		• o	• o
Alternative Groups		• p
Alternative Groups		• p
Anonymous Alternative Groups
Anonymous Alternative Groups
Atom-Atom mapping
Variable Attachment Positions

aa	Converted to the appropriate number of exact substituents

a	Free Sites counts of zero translated to "Substitution as drawn"; all other Free Sites values unsupported

b	Converted to the appropriated number of Free Sites

c	Substituent counts of greater than 5 are translated to "6 or more"

d	Converted to Wedged Hashed

e	Converted to Wedged

f	Converted to Racemic

g	Converted to a Single, with a positive charge applied to that atom at the base of the dative bond and a negative charge applied to the atom at the point of the dative bond

h	Interpreted by ISIS as unspecified cis/trans stereochemistry

i	Converted to Double

j	Converted to Normalized

k	Converted to S/D

l	Converted to Undefined

m	Only M, X, Q, A

n	Extensive list — see DARC manual

o	Truncated to the first 5 elements

p	Converted to G-Groups and possibly renamed; only 20 supported in one file


Chapter 10, Drawing With Templates - Overview
Overview

Template documents are collections of structures organized by structural type or functionality. A structure in a Template document is named a template. You can use an existing template instead of drawing the structure to shorten the time required to create documents.

The Template documents distributed with ChemDraw are stored in a directory named "cd_items" (Windows), or in a folder named "ChemDraw Folder" (Macintosh) that usually resides in the same folder/directory as the ChemDraw application.

In ChemDraw Pro you can define your own commonly used structures as templates. Any Template documents in the ChemDraw Folder are listed in the Windows menu in ChemDraw Pro.


The Template Tool

Several tools, including the Template tool, contain palettes from which you can select many different types of structures or objects. The triangle in the lower right corner of the picture of the Template tool indicates that this tool contains a palette. The Template tool has two levels: the first level displays the available Template documents, and the second level displays the templates within each Template document.

Figure 10-1 Template tool icon and file list

To display the available Template documents:

·	Point at the Template Tool icon in the Tools palette and hold down the mouse button.

A menu listing the Template documents appears. Template documents must be stored in the cd_items directory (Windows) or in the ChemDraw Folder (Macintosh)to appear in this menu.

NOTE: In ChemDraw Pro the pop-up menu is segmented if any Template documents are open for editing. The upper segment contains Template documents that are currently open for editing.

To display the templates available within a particular Template document:

·	Drag to the name of the Template document and continue holding the mouse button down.

A palette appears containing the available templates.

Figure 10-2 Bicyclics template displayed using the Template tool

More:

Choosing a Template


Choosing a Template

(Macintosh and Windows 3.1 and NT 3.5 users): To choose a template from a Template palette:

·	Point to the Template Tool icon and hold down the mouse button.

·	Drag to a Template document name and then to a template.

·	Release the mouse button to choose the highlighted template.

NOTE: In ChemDraw Pro (Macintosh only) when you choose a template, the template document containing the template is added to the Window menu. Choosing the document from the Window menu opens it for editing.

NOTE: When you display the Template palette that was last used, a blinking box appears around the currently selected template until you drag to another template.

(Windows 95 and Window NT 4.0 users): To choose a template from a Template palette:

·	Point to the Template Tool icon and click to display a list of template documents.

·	Point to the template document to display its contents.

·	Click the template you want to use.


Drawing with Templates

When you draw with templates, the first bond drawn determines the position of the template in a document window and all remaining bonds are drawn counterclockwise. The most nearly vertical bond on the leftmost atom is drawn first, from top to bottom. If there are two equivalent bonds, the atoms that are at a lower position are used to draw the first bond.

Figure 10-3 Drawing direction of template structures

Templates are automatically scaled to the document settings of the current document in the active window. Once a template is drawn in a document window, the structures or objects can be manipulated by standard drawing and editing methods.

To quickly draw a template:

·	Click in a document window.

The template is drawn centered around the pointer in the orientation that it appears in the Templates palette.

To quickly draw a template and fuse it with an existing structure:

·	Click an existing bond in a document window.

To deposit a template and create a spiro-linkage with an existing structure:

·	Click an existing atom in a document window.

To draw a template in a document window and control the size and orientation:

·	Drag from the beginning of the first bond in the template to the end of the first bond.

When you drag upwards the bulk of the template is drawn to the left, and when you drag downwards the bulk of the template is drawn to the right. Templates must contain at least one bond in order to be drawn by the dragging method.

More:

Drawing with the Same Template


Drawing with the Same Template

To draw another template of the same type:

·	Click the Template Tool icon to select it.

·	Draw the template in a document window.


Creating Templates and Template Documents

In ChemDraw Pro you can create new templates and add them to existing Template documents or create new Template documents.

To create a new Template document (Windows):

·	From the File menu, choose Open Special.

·	From the Open Special submenu, choose TEMPLATE.CTS.

Or, for the Macintosh:

·	From the Window menu, the New Template Stationery Pad.

A new and untitled Template window appears. The Template window is similar to a document window regarding the standard window elements, such as scroll bars. In addition, the Template window is divided into two halves by a moveable, horizontal line. The top half of the window is the Template panel that consists of individual Template panes where newly created templates will appear. The bottom half of the window is the drawing area where you can draw new templates.

NOTE: The templates you define are not limited to atoms and bonds. Templates can contain any ChemDraw object such as captions, boxes, arcs, orbitals, arrows, reaction mechanism symbols and curves. The ChemDraw objects in Template documents can also be colored. However, the colors will not appear in the Template tool pop-up palette. You can also paste pictures from other applications into a Template pane. Pasted objects are scaled to the current Template document settings. Templates must contain at least one bond in order to use the dragging method to draw in a document window.

Figure 10-4 A Template window

More:

Creating Templates

Orientation of Templates

Resizing Template Panes

Template Panels

Saving Template Documents


Creating Templates

 To create a new template:

·	Select a Template pane by clicking it.

·	Draw a structure or object in the drawing area of the Template window.

The structure appears in the Template pane as you draw. The tools in the Tools palette are used to draw a template in the drawing area of the Template window exactly as they are used to draw structures in the drawing area of a document window.

To select a different Template pane:

·	Click another Template pane.

When you select a Template pane, the contents of the pane appear in the drawing area.

Figure 10-5 Creating a template

As you define templates they become available for use in your document without having to save the Template document.

·	Point at the Template Tool icon in the Tools palette and hold down the mouse button.

The name of the new Template document appears in the pop-up menu.


Orientation of Templates

To make the templates that you create as easy to draw with as possible, it is recommended that you orient your structures so that the bond that establishes the position of the template, for instance the bond used for fusing, is leftmost and vertical. As discussed in "Drawing a Template" earlier in this chapter, the most vertical leftmost bond is drawn first. Refer to that section for examples.


Resizing Template Panes

To resize the Template panes in the Template panel:

·	Drag the Resize handle on the lower right corner of the Template panel.

The percentage the block of Template panes is enlarged or reduced appears in the Message area.


Template Panels

To increase the size of the Template panel:

·	Drag the Template dividing line.

To add a row of panes to the Template panel:

·	Select a Template pane.

·	From the Tools menu, choose Add Row.

The new row is added at the below the Template pane you selected.

To add a column to the Template panel:

·	Select a Template pane.

·	From the Tools menu, choose Add Column.

The new column is added to the right of the Template pane you selected.

To delete a row of Template panes from the Template panel:

·	Select a Template pane in the Row you want to delete and choose Delete Row from the Tools menu.

To delete a column of Template panes from the Template panel:

·	Select a Template pane in the column you want to delete.

·	From the Tools menu, choose Delete Column.

The column is removed and all other columns are moved to the left.


Saving Template Documents

To save a Template document and have it available in the Template pop-up menu and the Window menu:

·	From the File menu, choose Save As.

The Save File dialog box appears (Figure 10-6). The cd_items directory9- (Windows) or the templates file format are automatically selected.

Windows: Saving a Template document in the cd_items directory makes it accessible in the Open Special submenu and in the Template tools palette.

Macintosh: Saving a document in the ChemDraw Folder makes it accessible in the Windows menu and in the Template tools palette.

·	Type a name for the Template document and click the OK/Save button.

The Template document will be available for use each time you start ChemDraw Pro.


Chapter 12, Working with Page Layout - Overview
Overview

The presentation quality of your ChemDraw document is determined by how well the chemical structures and other objects are placed on the page, also called the layout. Effective layout of a drawing includes proper alignment of chemical structures and other objects, appropriate page size, and page orientation. This chapter discusses the methods and tools available to achieve these ends, which includes setup of the page and the use of the ruler, Crosshair, grouping, layering, aligning, and distributing commands.


Controlling the Drawing Area

The size of a document window is not necessarily the same as the size of the drawing area of the page. A document window, in most cases, actually covers only a portion of the drawing area.

More:

Enlarging the Drawing Area

Scrolling within a Document Window

Page Setup

Changing Perspectives


Enlarging the Drawing Area

To see more of the drawing area:

•	Point to a border or corner of a document window and drag to resize. Or, for the Macintosh, drag the Size box in the lower right corner of the document window.

When the pointer is correctly positioned for resizing, the pointer changes to a multi-sided arrow (the direction of the arrowheads indication the directions you can resize the window).


Scrolling within a Document Window

To move around the drawing area you can use the Scroll bars, Scroll boxes and Scroll arrows found on the right and bottom edges of a document window and the page up and page down arrow buttons on your keyboard. You can scroll as far as the edge of the drawing area.

To view different sections of the drawing area in a document window:

•	Click a Scroll arrow to move in small increments in that arrow’s direction.

•	Or, hold down the mouse button on a Scroll arrow to continuously scroll in that arrow's direction.

•	Or, click in the gray area above/below or to the left/right of the Scroll box to move in large increments in that direction.

•	Or, drag the vertical or horizontal Scroll box to move to the corresponding area of the drawing area.

.


Page Setup

The parameters that affect the size and curve of the drawing area are the page size, orientation, and margins. These parameters are specified using the Print/Page Setup dialog box. The Print/Page Setup dialog box and the options available will vary depending on the printer you have chosen (and, for the Macintosh, the version of the printer driver for that printer installed in your System Folder.)

To set the paper size, orientation and margins:

·	From the File menu, choose Print/Page Setup.

The Print Setup dialog box appears. The dialog box will appear slightly different depending on the printer and platform you have.

·	Select a page size.

The available paper sizes vary depending on the type of printer. Listed below are common sizes available. The page orientation you choose will determine which of the measurements is height and which is width:

Table 12-1 Common paper sizes

US Letter	8.5 x 11 inches
US Legal	8.5 x 14 inches
A4 Letter	21 x 29.7 centimeters
B5 Letter	17.6 x 25 centimeters
Tabloid	11 x 17 inches
International	8.5 x 12 inches
Computer paper	14 x 11 inches
To choose a paper size:

·	Select a paper size option/radio button.

More:

Orientation

Margins

Reduce or Enlarge

Saving Settings

Footer

35mm Slide Boundary Guides


Orientation

To choose the orientation of the page:

·	Select the vertical (portrait) or horizontal (landscape) orientation button.

The orientation of a document window will change to the orientation you have chosen. This is evident when the rulers are visible.


Margins

To change the margins for the paper size you have chosen:

·	Select the text next to the margin you want to change.

·	Type the new margin measurement.

The units of the margins are set in the Preferences dialog box. The paper size minus the margins determines the drawing area.

·	Click the OK button to exit with these changes.

NOTE: Most printers do not use other printers' Print/Page Setup settings; if you change printers (e.g. with the Chooser), you should check the Print/Page Setup settings for all of your documents.


Reduce or Enlarge

 Some PostScript printers include an option to reduce or enlarge your drawings by a variable percentage (25-400%). This option will scale all objects and text in the document window by the percentage specified. This is not a change in magnification, which is discussed later in this chapter. The size of objects is changed relative to the paper size, margins, and orientation you have specified.

The enlarge or reduce option is useful for changing the size of the available drawing area, while keeping the images on the screen at the normal size when you are drawing. Another use for this option is if you have drawn structures to fill the area of the page specified using one printer, and then changed to another printer that requires larger margins; in this case your picture will seem to disappear off the edge of the page. You can reduce the size of the image using the reduce option and the picture will again appear in the document window.


Saving Settings

You can save Print/Page Setup settings in a Style Sheet/Stationery Pad. Whenever you open a Style Sheet/Stationery Pad, these settings are automatically used. The Print/Page Setup settings are saved in addition to the Text settings, Drawing Settings, and, the Color Palette. See “Saving Customized Settings” in Chapter 1, ChemDraw Basics, to learn more about using Style Sheets/Stationery Pads.


Footer

You can have a footer appear at the bottom left of your document window that contains the name of the document and the date and time it was last changed. The footer cannot be edited.

Preferences Guide

Include Footer

To have a Footer appear at the bottom of all ChemDraw documents:

·	From the File menu, choose Preferences.

·	Select the Include Footer check box.

·	Click the OK button.

Changes to this preference will affect all documents.


35mm Slide Boundary Guides

If you are planning to make 35mm slides from a hard copy of a ChemDraw document, or by taking a screen shot, you can display boundary lines that appear on your screen positioned at 7 inches and 10.5 inches to match the 2:3 ratio for the 35 mm slide format. These guides help you keep your drawing within this region to maintain the proper ratio, but will not be printed. The drawing area of the page must be at least 7 x 10.5 inches for these boundary lines to be visible.

Preferences Guide

Show 35mm Slide Boundary Guides

To display the 35mm slide boundary lines:

·	From the File menu, choose Preferences.

·	Select the Show 35mm Slide Boundary Guides check box.

·	Click the OK button.

Two 35mm Slide Boundary Guides appear in the same orientation you have chosen in the Print Setup dialog box. These guides will appear in every document.

Changes to this preference will affect all documents.


Changing Perspectives

Sometimes you may need to get a close-up view of certain objects in your reaction scheme, such as arrows and reaction mechanism symbols, to make sure that objects are properly positioned. At other times, you may want to reduce your view so that you can move groups of objects around the page. You can increase and decrease the magnification for performing these functions using the Magnify and Reduce commands in the Tools menu.

More:

Magnify

Actual Size

Reduce

Show Page


Magnify

To magnify the view on an object:

·	Select the object around which you want to magnify your view.

·	From the Tools menu, choose Magnify.

The magnification occurs around the center of the selected object. The magnification appears in the Message area of a document window. You can continue to magnify your view three more times to a maximum of 400%.

Figure 12-2 Message Area displaying a magnification

The last object drawn will be the center point of the magnification if you do not select an object in a document window.


Actual Size

To return to the actual size from any other magnification:

·	From the Tools menu, choose Actual Size.

The view is returned to the original size. The Message area is empty.


Reduce

To reduce the magnification:

·	Select an object around which you want to reduce the magnification.

·	From the Tools menu, choose Reduce.

The reduction in magnification appears in the Message area of the document window.

Figure 12-3 Message Area displaying a reduction

You can reduce the magnification until the entire page fits on the screen. The size of your monitor will determine the low end for this reduction. For instance, you can reduce the magnification in one increment to 71%, on a 16 inch monitor, whereas you can reduce the magnification in three increments to 35%, on a 9 inch monitor.

In the reduced view, you can continue to use all of the drawing tools. In particular, you can use a selection tool to rearrange the drawing in order to take better advantage of the space available.


Show Page

The Show Page command is equivalent to repeatedly choosing the Reduce command until the entire page is visible in the document window.

To view the entire drawing area in a document window at once:

·	From the Tools menu, choose Show Page.

The Message area shows the reduction in magnification that was required to have the entire page appear on the screen. This magnification also reflects the minimum magnification that you can obtain using the Reduce command.


Arranging Objects

This section describes methods for positioning, aligning, and layering objects in a document window.

More:

Using Rulers

Using the Crosshair

Centering on a Page

Aligning Objects

Distributing Objects

Front to Back Ordering


Using Rulers

You can use the rulers to position objects a measured distance away from some reference point or create objects of an approximate size. The units used for the ruler are set in the Preferences dialog box, where you have the choice of inches, centimeters or points.

More:

Show Rulers

Hide Rulers


Show Rulers

To display the rulers:

·	From the Tools menu, choose Show Rulers.

A check mark appears next to the Show Rulers command, and the rulers appear along the top and left edges of a document window.

Figure 12-4 Rulers in a document window

As you move the pointer, Ruler Guides appear on each ruler, indicating the position of the pointer.

Figure 12-5 Ruler guides when pointing

Ruler guides also appear when you drag selected objects. In this case, however, there are two Ruler guides that bracket the object. With this bracketing you can quickly establish the height and width of the selected object(s).

Figure 12-6 Ruler Guides when moving a selection


Hide Rulers

To Hide the rulers:

·	From the Tools menu, choose Show Rulers.

The check mark disappears.


Using the Crosshair

You can use the Crosshair to align objects relative to each other, and to space objects a consistent distance apart. The axes of the Crosshair can be moved within a document window.

More:

Show Crosshair

Moving the Crosshair

Aligning Objects using the Crosshair

Hide Crosshair


Show Crosshair

To show the Crosshair:

·	From the Tools menu, choose Show Crosshair.

A check mark appears next to the Show Crosshair command and the Crosshair appears within a document window.

To assist you in aligning objects, the Crosshair includes grid lines which extend from the major division marks on each Crosshair axis.

Figure 12-7 The Crosshair

You can also show the Rulers while the Crosshair is displayed so that you can see the unit measurement associated with each of the divisions on the Crosshair axes.


Moving the Crosshair

To move the Crosshair:

·	Position the pointer where the Crosshair axes intersect.

When the pointer is near to the center of the Crosshair, it changes to an arrow

·	Drag the Crosshair.

To constrain the movement of the Crosshair to the X or Y direction:

·	Alt+drag (Windows) or Command+drag (Macintosh) the Crosshair.


Aligning Objects using the Crosshair

To use the Crosshair to align objects:

·	Move the Crosshair axes and align it with the object.

·	Or, select an object and drag it until it is aligned with either axis of the Crosshair, or a grid line.

In either case, if a bond or side of the object is parallel to one of the axis, it will disappear when it is exactly positioned over a Crosshair axis.

To align another object on the Crosshair.

·	Select a second object.

·	Drag the second object to the Crosshair axis or grid line and align it to the first.

You can also move selected objects in small increments to align them with the Crosshair using the Arrow keys available on some keyboards:

To move 1 point in the direction of an Arrow key (1 point equals 1/72 inch, or 0.035 cm):

·	Select the object(s) and then press an Arrow key.

To move 10 points using the Arrow key, for example, to the right:

·	Press Ctrl+Right Arrow (or Option+Right Arrow).


Hide Crosshair

To hide the Crosshair:

·	From the Tools menu, choose Show Crosshair.

The checkmark next to the Show Crosshair command disappears.


Centering on a Page

To center an object (or group of objects) at the center of the page:

·	Select the object you want to center using a selection tool.

·	From the Object menu, choose Center on Page.

The selected objects move so that the center of the Selection rectangle is positioned at the center of the page.


Aligning Objects

There are several align commands available in the Align submenu from the Object menu. Choose any of these commands to align objects relative to each other.

To align two or more objects:

·	Select the objects with a selection tool.

·	From the Align submenu, choose one of the Align commands.

If you select only part of a structure or group with a selection tool, only that part is used for the alignment operation, but the entire structure or group is moved.

Figure 12-9 Aligning structures

select		choose Left Edges


Distributing Objects

There are two distribute commands available in the Distribute submenu in the Object menu. Choose one of these commands to distribute objects horizontally or vertically and an equal distance apart. In combination with the align command, you can easily clean up the appearance of a reaction.

To distribute 3 or more objects:

·	Select the 3 or more objects to distribute.

·	From the Distribute submenu in the Object menu, choose Vertically or Horizontally.

The space between the objects is equalized. The position of objects in your selection that are rightmost and leftmost (or uppermost and lowermost) remain unchanged.

Figure 12-10 Spacing structure evenly along the x-axis

draw rough diagram

choose Distribute Horizontally


Front to Back Ordering

The front to back ordering is a useful method for changing the orientation of one object relative to another object within the same picture layer.

More:

Picture Layers

Send to Back

Bring to Front


Picture Layers

There are three layers within a ChemDraw document. From back to front, they are: imported pictures, graphical ChemDraw objects and text. The ordering of these layers cannot be changed. However, the front to back ordering of objects within each layer can be specified with the Bring to Front and Send to Back commands in the Object menu.

For example, if an imported picture is dragged onto a ChemDraw structure, the structure will not be hidden since the imported picture resides in the backmost layer.

An imported picture is any picture pasted into a ChemDraw document from another application such as a molecular model or a graph from a graphing application. The picture can be imported into the ChemDraw document by using the Paste command. A graphical ChemDraw object is any structure or object created within ChemDraw, excluding text. Text, including both atom labels and captions, is always the frontmost layer.

NOTE: When you point at an imported picture, a highlight box appears around the periphery of the object that helps distinguish it from a graphical ChemDraw object. Text also has this type of highlight box


Send to Back

To place one object behind another within a layer:

·	Select the object that you want to send to the back.

·	From the Object menu, choose Send to Back.

The selected object appears behind all other objects in the same layer.

Figure 12-11 Changing layering of p-orbitals

select		choose Send to Back


Bring to Front

To place one object in front of another within a layer:

·	Select the object that you want to move forward.

·	From the Object menu, choose Bring to Front.

The selected object now appears in front of all other objects in the same layer.


Chapter 13, Sharing Information - Overview
Overview

This chapter describes several ways to transfer information between ChemDraw and other applications. ChemDraw includes many of the standard system commands for transferring information within ChemDraw documents, between ChemDraw documents and between documents created using other applications via the Clipboard, drag and drop, object embedding and file formats.


Working Between ChemDraw Documents

You can use the Clipboard or Drag and Drop to transfer ChemDraw pictures to other ChemDraw documents.

More:

Copy

Cut

Paste

Drag and Drop

Autoscaling


Copy

To place a ChemDraw picture on the Clipboard:

·	Select the objects to copy using a selection tool.

·	From the Edit menu, choose Copy.

A copy of the selected objects is placed on the Clipboard. The selected objects in a document window remain unchanged.


Cut

To place a copy of the ChemDraw objects on the Clipboard and remove the objects from a document window:

·	Select the objects to remove using a selection tool.

·	From the Edit menu, choose Cut.

A copy of the selected objects is placed on the Clipboard. The selected objects are removed from a document window.


Paste

To paste the contents of the Clipboard into a ChemDraw document window:

·	From the Edit menu, choose Paste while a selection tool is selected.

·	The contents of the clipboard are placed in the center of the active document.

If the Clipboard contains ChemDraw structures, the pasted information is scaled to the settings in the current document.

To view the contents of the Clipboard:

·	Return to the Program Manager or File Manager and start the Clipboard Viewer. Or, for the Macintosh, choose Show Clipboard from the Edit menu.

Refer to your operating system documentation for information on using the Clipboard.

NOTE: You can paste the contents of the Clipboard into another application by the same procedure. Refer to your application documentation for additional information specific to the application. Macintosh: If you are pasting the ChemDraw picture in a document from which you are planning to print to a PostScript printer, refer to the section "Including PostScript" later in this chapter for important information.


Drag and Drop

Another way to copy information between ChemDraw documents and other applications' documents is through drag and drop. This feature provides streamlined copy and paste that bypasses the Clipboard.

NOTE: If you are using the Macintosh version and have system software prior to System 7, you will need the Drag and Drop extension loaded for this to work.

To copy and paste information between ChemDraw documents using Drag and Drop:

·	Select an object or structure in a ChemDraw document.

·	Drag the selection into another ChemDraw document window.

The selection is copied to the destination ChemDraw document.

To copy and paste a selection to another application's document:

·	Select an object or structure in a ChemDraw document.

·	Drag the selection into another application's document window.

The selection is copied to that application's document.

NOTE: The other application, like ChemDraw, must support Drag and Drop for this feature to work.

Using Drag and Drop, you can also create clipping files (Macintosh) or scrap files (Windows 95 only).

To create a clipping file or a scrap file:

·	Select an object or structure in a ChemDraw document.

·	Drag the selection out of the ChemDraw document window onto the desktop.

A clipping file or a scrap file is created on your desktop.

NOTE: (Macintosh only) You must have the Clipping Extension installed to create a clipping file if you are using system software prior to 7.5.

To view the information within a clipping file or a scrap file:

·	Double-click the file's icon.

A window appears showing the ChemDraw picture. Click the close box to close the clipping file's window.

To use the contents of a clipping or scrap file in a document:

·	Drag the clipping or scrap file into an open window of an application that supports Drag and Drop, such as an open ChemDraw document window.

The contents of the clipping or scrap file are copied to the open window. The clipping or scrap file remains unchanged.


Autoscaling

When you transfer ChemDraw objects via the Clipboard or drag and drop from one ChemDraw document (the source document) to another ChemDraw document (the destination document), the objects are scaled to match the document settings of the destination document. This automatic scaling assures that the objects being transferred will match the settings of the current document.

Bonds

All bonds drawn in the source document using the values specified in the Drawing Settings dialog box will be changed to use the Drawing Settings in the destination document.

Any bond that has been resized in the source document will be scaled in the destination document. The scale factor used is based on the ratio of the bond's length after resizing (source) to the Fixed Length in the Drawing Settings dialog box (source). This scaling process maintains the proportions in the destination document that are present in the source document. All values in the Drawing Settings dialog box are scaled in this same manner.

For example, in a source document, the Fixed length is set to 1.0 cm. A benzene ring is resized in the source document to 200%, so the bond length is actually 2.0 cm, which represents a ratio of 2.0 cm/1.0 cm or a scale factor of 2. A destination document has a fixed length set at 1.7 cm. When the benzene ring is pasted into the destination document, the bonds will be scaled by a factor of 2 to a final bond length of 3.4 cm.

Atom Labels

Atom labels are scaled in the same fashion as bonds discussed in the previous section.

For example, the atom label font size is set to 16 points in Label Text Settings dialog box of the source document. One or two atom labels in the source document are resized to 8 points, which represents a ratio of 8/16 or a scale factor of 0.5. The destination document has an atom label font size of 14 points set in the Label Text Settings dialog box. When the atom label is pasted into the destination document, the font size is scaled by a factor of 0.5 to give a final atom label font size of 7 points.

Captions

Captions are always autoscaled based on the ratio of the fixed length in the destination document to the fixed length in the source document times the caption font size (the font size of the caption can be any size and is not related to the setting in the Caption Text Settings dialog box, as discussed for atom labels). This assures that captions are always in proportion to the bonds with which they are pasted.

For example, If the source document has a fixed length of 1.0 cm and the destination document has a fixed length of 2.0 cm, and the caption you are pasting is 12 points, then the resulting caption size after autoscaling is (2.0 cm /1.0 cm ) x 12 points = 24 points.

Non-bond Objects and Color

All objects that are not affected by settings in the various Document Settings dialog boxes, such as arrows, boxes and so on, will be scaled to maintain the same proportions to bonds that were present in the source document.

With the exception of the foreground and background color, the other colors present in the selection to be pasted are added to the destination document's Color Palette if they are not already present (up to a maximum of 20 total colors). The background color in the destination document remains unchanged, and all objects colored using the foreground color are changed to match the foreground color in the destination document.

Pasting to an Empty Document Window

If you are pasting a ChemDraw drawing to an empty ChemDraw document, and the settings between the documents are different, the following dialog box appears:

To change the settings in the destination document to match the settings in the source document:

·	Click the Change Settings button.

All of the settings in the various document settings dialog boxes in the destination document (the document being pasted to) are changed to match those of the source document (the document from which it is being copied). All of the colors in the Color Palette of the destination document, including the Foreground and Background color are changed to those specified in the source document.

To scale the objects from the source document to the settings in the destination document:

·	Click the Don't Change button.

The settings from the source document (the document being copied from) are scaled to those in the destination document (the document being copied to) using the ratios discussed previously.

NOTE: If the source document was created in a version of ChemDraw that is earlier than version 3.0, the name of the document will appear as "Unknown" in the dialog box.


Embedding Objects

For making changes to ChemDraw pictures that are pasted in other types of documents, ChemDraw supports the Object Linking and Embedding (OLE) protocol on Windows and Publish and Subscribe on the Macintosh.

NOTE: ChemDraw running under Windows is an OLE server, which means it can create OLE objects that can be copied and pasted into other OLE client applications.

More:

OLE (Windows Only)

Publishers, Subscribers, and Editions (Macintosh only)

Transferring PostScript (Macintosh only)


OLE (Windows Only)

When a picture is transferred from ChemDraw into another type of document that supports OLE, you can open the picture (often by double-clicking it) and the picture appears in a ChemDraw document window. Any changes you make within the ChemDraw document window are automatically reflected in the other document when you close the ChemDraw window.

For example, to edit a ChemDraw picture pasted into Microsoft Word for Windows version 6.0 or later.

·	Double-click the ChemDraw picture that is pasted into a Microsoft Word document.

The ChemDraw application will launch if it is not already running. The picture opens in a window titled "From Microsoft Word". You can use all the tools available in ChemDraw to edit the picture. When you have finished making changes:

·	From the File menu, choose close.

The ChemDraw document window disappears and the picture in the Microsoft Word document is updated with any changes you made.


Transferring PostScript (Macintosh only)

To obtain the highest quality drawings possible on a PostScript printer, ChemDraw creates both a screen representation and a PostScript representation of your drawing. PostScript is a page-definition language used to describe pictures. Many printers, including most Apple LaserWriter printers, use PostScript to create high quality output.

The PostScript representation of a ChemDraw picture is composed of two parts, the PostScript commands and the ChemDraw Laser Prep. The ChemDraw Laser Prep contains specific instructions that enable the laser printer to interpret the PostScript commands contained in a ChemDraw document.

If you are transferring a ChemDraw picture to another application on the Clipboard, through an edition file, or through EPS files you need to specify that both the PostScript commands and the ChemDraw Laser Prep be sent along with the picture. You can specify this in the Preferences dialog box. There are several different situations that require either one or both to be selected.

Preferences Guide (Macintosh)

Include PostScript; Include ChemDraw Laser Prep

If you are transferring several pictures to other applications and you also have access to ChemDraw.

·	From the File menu, choose Preferences

·	Select Include PostScript and deselect Include ChemDraw LaserPrep.

To print the document(s):

·	Choose Initialize LaserWriter from the File menu within ChemDraw.

This command sends the ChemDraw Laser Prep directly to your printer. You do not need to send this command for each document you are printing, since the ChemDraw Laser Prep remains in the printer's memory until the printer is turned off or reinitialized.

If you are transferring only a few pictures to another document, or if you are transferring pictures to a document in a remote location whose printer cannot be initialized by ChemDraw:

·	Select Include PostScript and Include ChemDraw Laser Prep in the Preferences dialog box.

In this instance both the PostScript commands and the ChemDraw Laser Prep are transferred with each picture. ChemDraw pictures transferred in this manner can be printed independently of ChemDraw. The ChemDraw Laser Prep file adds approximately 11K to 12K to the size of each picture.

If you do not check the Include PostScript checkbox when printing to a PostScript printer ChemDraw sends QuickDraw commands to the printer. See "Print Quality" in Chapter 1, ChemDraw Basics, for more information about QuickDraw.

If you do not have access to a PostScript printer, or you are printing to a non-PostScript printer, or you are transferring ChemDraw pictures to a drawing program that does not use PostScript commands (such as a Paint program):

·	Deselect both Include PostScript and Include ChemDraw Laser Prep in the Preferences dialog box.

For best print quality under all circumstances (at the expense of slightly larger files) you are encouraged to check both the Include PostScript and Include ChemDraw Laser Prep preferences. This will give you the greatest flexibility if you give your document to someone else or later want to print it on a PostScript printer.


Publishers, Subscribers, and Editions (Macintosh only)

This section describes how to share information through a dynamic link between a ChemDraw document and one or more other application documents using the publish, subscribe and edition features. For example, you can link a ChemDraw document to another ChemDraw document and also to a word processing program.

To create a link, you designate a portion of a ChemDraw document as a publisher and save a picture of the publisher in an edition file. You can then designate an area within a document as a subscriber and also link to this edition file. Changes made to the publisher will update the edition file, which in turn will update the subscriber. Updating can be automatic or manual depending on the options you choose. The subscriber document does not need to be open for this updating process to occur, as updating is done in the background.

NOTE: All colors, except for the Background Color, are contained within an edition file. The Background Color is always removed.

NOTE:  In ChemDraw Pro, you cannot publish or subscribe from a Template document.

More:

Creating a Publisher

Subscribing to an Edition File

Publisher Options

Subscriber Options

The Edition File


Creating a Publisher

To create an edition file, you first need to identify the part of your ChemDraw document that you want to publish:

·	Select the objects(s) to publish using a selection tool.

To specify where to create the edition file containing a picture of the selected objects:

·	From the Edit menu, choose Create Publisher

The Create Publisher dialog box appears where you can specify the name of the edition file, and the folder and disk where you want to place the file.

The Create Publisher dialog box is the same as the Save File dialog box with the addition of a Preview section on the left side. A picture of the portion of the document that you are publishing appears in the Preview section.

·	Type a name for the edition file, and choose a folder to save it in.

·	Click the Publish button.

The Create Publisher dialog box disappears. The object you selected is enclosed in a gray rectangle called a Publisher border.

Figure 13-3 A cyclohexane structure enclosed in a publisher border

The entire area contained within the borders of the publisher is included in the edition file. Any object or part of an object that is inside the borders of the publisher will appear in any document that subscribes to the edition file. The publisher border is an object; and so it can be selected, moved and resized independent of its contents, using a selection tool.

To resize a publisher border without changing its height to width ratio:

·	Select the publisher border by clicking with a selection tool.

·	Drag the resize handle on the Resize handle.

To resize a publisher border in the X or Y direction only:

·	Hold down the Command key and drag the Resize handle.

When the edition file is updated, the two carbons of the cyclopentane ring will appear in any document that subscribes to the edition file.

Publisher borders appear only on the screen. They are not printed.

To hide the Publisher borders:

·	From the Edit menu, choose Show Borders.

The checkmark disappears as well as the publisher border.


Subscribing to an Edition File

To subscribe to the contents of an edition file:

·	From the Edit menu, choose Subscribe To.

The Subscribe To dialog box appears where you can select the edition file to which you want to subscribe.

The Subscribe To dialog box is the same as the Open File dialog box with the addition of a Preview section on the left side.

·	From the directory listing, select the edition file you want to subscribe to.

A picture of the contents of the edition file appears in the Preview section.

·	Click the Subscribe button.

The Subscribe To dialog box disappears. The most recent edition appears in the document window enclosed in a gray rectangle called a Subscriber border.

A subscriber is an object that can be selected, moved and resized using a selection tool. If you resize a subscriber, each time an edition file is updated the contents will appear resized. The Subscriber border appears only on the screen. It is not printed.

To hide the Subscriber borders:

·	From the Edit menu, choose Show Borders.

The checkmark disappears as well as the subscriber border.


Publisher Options

You can use the Publisher Options command to specify when an edition file is updated with changes made to the publisher and to display other information about the edition file.

To open Publisher Options:

·	Select a publisher by clicking the Publisher border using a selection tool.

·	From the Edit menu, choose Publisher Options.

or

·	Double-click the Publisher border.

The Publisher Options dialog box appears.

Publisher to

To display a pop-up menu listing the location of the edition file linked to the publisher:

·	Point to the Publisher to pop-up menu and hold down the mouse button.

Send Editions

You can specify when a publisher sends a new edition to an edition file by setting options within the Send Editions section. In ChemDraw, each time a publisher updates an edition file, the edition file contains the most up-to-date picture of the object(s) contained within the publisher border.

To update an edition file automatically each time the document is saved:

·	Select the On Save radio button.

By using this option you do not need to remember to send updates every time you make changes to objects contained within the Publisher border.

To have more control over which revisions of the publisher will be sent to the edition file:

·	Select the Manually radio button.

To update the edition file when the Manually radio button is selected:

·	Click the Send Edition Now button.

The Latest Edition is the last date and time the edition file for the publisher was updated. When the Manually radio button is selected, the Last Change appears below the Latest Edition time and refers to the last date and time that changes were saved in the edition file.

Cancel Publisher

To delete a publisher and its corresponding edition file:

·	Click the Cancel Publisher button.

An alert appears asking you if you are sure that you want to remove the selected publisher. When you cancel a publisher, the publisher border around the picture is removed from the document. The edition file is deleted when the document is saved.


Subscriber Options

You can use the Subscriber Options command to specify when a subscriber is updated with the contents of the edition file.

·	Click the Subscriber border using a selection tool.

·	From the Edit menu, choose Subscriber Options.

·	Or, double-click the Subscriber border.

The Subscriber Options dialog box appears.

Subscriber to

To display a pop-up menu showing the location of the edition file linked to the subscriber:

·	Point to the Subscriber to pop-up menu and hold down the mouse button.

Get Editions

You can specify when a subscriber receives the updated edition by setting the options within the Get Editions section.

To update the subscriber automatically each time the document is opened and each time the edition file is updated:

·	Select the Automatically radio button.

To specify each time the subscriber will be updated with the most recent version of the edition file:

·	Select the Manually radio button.

To update the subscriber when the Manually radio button is selected:

·	Click the Get Edition Now button.

The Latest Edition Time is the last date and time that the edition file for the selected subscriber was updated. When the Manually radio button is checked the Last Received time appears below the last edition time. The Last Received time is the date and time the contents of the edition file were used to update the subscriber.

Open Publisher

To open the document containing the publisher:

·	Click the Open Publisher button.

Cancel Subscriber

To break the connection between the selected subscriber and the edition file.

·	Click the Cancel Subscriber button.

An alert appears asking you if you are sure that you want to remove the selected subscriber. When you break the connection, the subscriber will be removed, but the picture will remain in your document.


The Edition File

To display the contents of an edition file:

·	Select the edition file icon in the Finder.

Figure 13-4 Edition file icon

·	From the File menu, choose Open, or double-click the icon.

A window appears containing a picture of the contents of the edition file.

Figure 13-5 Window containing contents of edition file

NOTE: The word in the lower left corner refers to the type of information contained within the edition file, in this instance it is PICT.

Open Publisher

To open the document containing the publisher linked to this edition file:

·	Click the Open Publisher button.


Importing and Exporting

There are two ways to transfer ChemDraw pictures to and from other applications: using different file formats, and using the Clipboard. File formats are useful for saving and opening the contents of a ChemDraw document for transfer to other chemistry, word processing and desktop publication applications on the same or a different computer. Example output files for chemistry file formats are shown in the on-line help file under the topic "Chemistry File Formats". The Clipboard, as discussed earlier, is useful for transferring part or all of the information within an active document window between applications on the same computer or a networked computer. In ChemDraw Pro, the Clipboard is extended for use in transferring information to other chemistry applications as SLN strings, SMILES strings and in ISIS format.

More:

Exporting via the Clipboard

Creating SMILES Strings

Paste SMILES via Clipboard

Creating SLN Strings


Exporting via the Clipboard

It is common to copy structures to the Clipboard for pasting into another chemistry application for further analysis or storage. To assist in the process, ChemDraw includes several formats on the Clipboard during a normal copying operation. Below are the supported by ChemDraw's Clipboard.

ChemDraw 4.5 (*.cdx)

ChemDraw 3.5 (*.chm)

PICT (Macintosh only)

WMF (*.bmp, Windows only)

PostScript (Macintosh only with appropriate preferences turned on)

ISIS/Sketch (SKC)

MDL MolFile (when no arrow is in the selection)

RXN File (when an arrow is in the selection)

DARC F1

Each of these formats is briefly described in the next section under file formats. In addition, Chapter 9, Drawing Query Structures includes some additional information as to what information is and is not copied.

To export a file using the Clipboard:

·	Select the structure using a selection tool.

·	From the Edit menu, choose Copy.

The structure is copied to the Clipboard. For large structures you may see a status bar indicating the progress.

In addition, you can choose one of several commands for created text string representations of selected structures that are copied to the Clipboard. These include SMILES and SLN strings.


Creating SMILES Strings

A SMILES string is a way of describing a chemical structure in a line of text, similar to the Wiswesser Line Notation used many years ago. Several software packages use SMILES strings as a compact means of entering and storing chemical structure information.1

For example, to create the SMILES string for the following structure:

·	Select the structure using a selection tool.

·	From the Copy As submenu in the Edit menu, choose SMILES.

The SMILES string corresponding to the trans-2-amino-cyclohexanol molecule is transferred to the Clipboard.

To display the SMILES String:

·	Switch to the Program Manager or File Manager and start the Clipboard Viewer.

Figure 13-6 Converting a structure into a SMILES strings

structure
N[C@@H]1[C@H](O)CCCC1
SMILES string
Once the SMILES string is on the Clipboard, you can transfer it to another application that can interpret and manipulate SMILES strings.

If you select more than one structure in ChemDraw, and choose Copy SMILES from the Edit menu, the SMILES string for each structure will be copied to the Clipboard and separated from the previous SMILES string by a period.

Figure 13-7 Converting two structures into SMILES strings

structures
N[C@@H]1[C@H](O)CCCC1.OC2=CC=C(N)C=C2
SMILES string
SMILES supports an alternate notation for aromatic structures using lowercase letters. ChemDraw will generate this type of SMILES string for any structure drawn with explicit aromatic bonds, either by using the Aromatic bond type in the Atom Properties dialog or by placing a circle within any ring structure

Figure 13-8 Alternative notation for aromatic structures

structures
NC1=CC=C(C=C1)O.Nc2ccc(O)cc2
SMILES string


Paste SMILES via Clipboard

If you have a SMILES string, a way of describing a chemical structure in a line of text, then you can automatically convert that text string into a ChemDraw structure.

·	Select the SMILES string using the Text tool.

·	From the Edit menu, choose Copy.

·	From the Paste Special submenu in the Edit menu, choose SMILES.

Your SMILES string is drawn as a structure.

NOTE: Paste SMILES uses the same routines as the Clean Up structure command. For more information about this command see "Structure Clean Up".


Creating SLN Strings

Similar to creating a SMILES string, you can copy a ChemDraw structure to the Clipboard as an SLN string for export to a TRIPOS application.

·	Select a structure.

·	From the Copy As submenu in the Edit menu, choose SLN.

The Structure is copy to the clipboard as an SLN String.

Figure 13-9 Cyclohexane structure and the resulting SLN string on the Clipboard

structure

C[1]H2CH2CH2CH2CH2CH2@1

SLN string


Exporting and Importing using File Formats

Many applications can use the information contained within a ChemDraw document that has been saved in one of the other file formats provided with ChemDraw or ChemDraw Pro. File formats are available in a pop-up menu (drop-down list) at the bottom of the Open and Save dialog boxes. This section briefly discusses the formats that are available.

To export a file:

·	From the File menu, choose Save As.

In the Save As dialog that appears do the following:

·	Type a name for the file and choose a location in which to save it.

·	Select a file format from the bottom of the dialog box.

·	Click the OK (Windows) or Save button (Macintosh).

A copy of the current document is saved in the format you specified. The current document remains unchanged.

This remainder of this section briefly (in alphabetical order) discusses the formats that are available.

NOTE: Some file formats do not support atom labels that contain nicknames (Me, Ph) or structural fragments (CH2CH2CH3, COOH). When saving in these formats, ChemDraw automatically expands all atom labels (see "Expand Label" in Chapter 8, Advanced Drawing Techniques, for more information) and saves the file using the expanded form. The following formats are affected in this way: Connection Table DARC F1 DARC F1 Query MDL MolFile MSI MolFile ISIS RXN SMD

More:

CD Template (*.ctp, *.ctr)

ChemDraw (*.cdx)

ChemDraw 3.5 (*.chm)

ChemDraw 2.0 and ChemDraw 2.1 (*.chm)

ChemDraw Stationery/Style Sheet (*.cds)

Connection Table (*.ct)

DARC-F1 Format *.f1d (Export only)

DARC-F1 Query *f1q (Export only)

Encapsulated PostScript (Text) (Macintosh) PostScript, *.eps (Windows) (both Export only)

Encapsulated PostScript (Macintosh)

GIF Image *.gif (Export only)

ISIS/SKC and ISIS/TGF

{ [image] /Reactions (*.rxn)

MDL MolFile (*.mol)

Molecular Simulations MolFile (*.msm)

PICT (Macintosh)

PICT scaled 4X (Macintosh)

SMD

Template Style Sheet (*.cts)

Windows Metafile (Windows Only) (*.bmp)

TIFF (*.tif)

PNG (*.png)


CD Template (*.ctp, *.ctr)

The CD Template file format is used for saving template documents that will appear in the template pop-up menu (when stored in the cd_items directory (Windows) or the ChemDraw Folder (Macintosh)).


ChemDraw (*.cdx)

The ChemDraw file format is the native format for ChemDraw version 4.0 and 4.5. This is a public tagged file format that stores information about a ChemDraw structure in a series of data blocks. This format is designed to be easily generated and interpreted by other programs. This format accurately stores anything that can be drawn in ChemDraw.


ChemDraw 3.5 (*.chm)

ChemDraw 3.5 file formats are used for saving or opening ChemDraw documents using the version 3.5.x of ChemDraw. These documents can also be opened in versions 3.0, 3.0.1, 3.0.2, and 3.1 of ChemDraw as long as atom properties are not used in the files.

NOTE: When you save a ChemDraw version 4.0 file in one of these formats, all features specific to version 4.0 are lost. For instance, multi-attached atom labels, variable attachment points, and multicenter bonds will not be saved.


ChemDraw 2.0 and ChemDraw 2.1 (*.chm)

ChemDraw 2.0 and ChemDraw 2.1 file formats are used for saving or opening ChemDraw documents using the version 2.x file format of ChemDraw for Macintosh.

NOTE: When you save a ChemDraw version 4.0 file in one of these formats, all features specific to version 4.0 are lost. For instance, color, dative bonds and shaded orbitals will not be saved.


ChemDraw Stationery/Style Sheet (*.cds)

ChemDraw Stationery file format is used for saving document settings and other objects. ChemDraw Stationery file format 1;See the section titled "Saving Customized Settings" in Chapter 1, ChemDraw Basics, for more information.


Connection Table (*.ct)

The Connection Table file format is a simple format that saves a list of atom connectivities in terms of an element, serial number, X and Y coordinates, bond order and bond type. This is a common format used for exchanging information between many chemistry applications.


DARC-F1 Format *.f1d (Export only)

The native file format for storing structures in the Questel DARC system.


DARC-F1 Query *f1q (Export only)

The native file format for storing queries in the Questel DARC system.


Encapsulated PostScript (Text) (Macintosh)PostScript, *.eps (Windows) (both Export only)

Encapsulated PostScript (Text) files, also referred to as EPS (Text), are ASCII text files containing the scalable PostScript representation of a ChemDraw picture that can be opened using other platforms and applications and platforms. No preview is included in this type of EPS file. Thus, programs that do not support the display of raw PostScript can only print, not view an image on screen.

EPS files are commonly used for sharing ChemDraw pictures with desktop publishing applications such as Adobe PageMaker and QuarkXPress.

All colors are saved in the EPS file except for the Background color.

NOTE: To save an EPS file with a colored background, create a large colored rectangular box using the Drawing Elements tool and choose Send to Back before saving the file.. To learn about drawing boxes, see “Boxes”, in Chapter 6, Drawing Arrows, Arcs and Other Shapes. To learn about adding color to objects, see “Working with Color” in Chapter 8, Advanced Drawing Techniques.


Encapsulated PostScript (Macintosh)

Encapsulated PostScript (Macintosh) files, also referred to as EPS (Mac) files, contain both the scaleable PostScript representation and the QuickDraw representation of a ChemDraw picture that other Macintosh applications can translate and view. ChemDraw pictures saved in EPS (Mac) file format can be opened by various illustration, desktop publishing and desktop presentation software packages on the Macintosh.

EPS (Mac) files created by earlier versions of ChemDraw can be opened by ChemDraw version 4.0.

All colors are saved in the EPS file except for the Background color.

NOTE: To save an EPS file with a colored background, create a large colored rectangle and choose Send to Back before saving the file.


GIF Image *.gif (Export only)

You can save your ChemDraw document in the graphics interface format, GIF. This file format is useful for working with the hypertext markup language (HTML) used in displaying information on the World Wide Web. A GIF image can be displayed directly on a Web page rather than having to download the picture for viewing in a Helper application.

ChemDraw always saves GIF files according to the 89a specifications with transparent backgrounds.


ISIS/SKC and ISIS/TGF

In addition to Clipboard compatibility, you can also save a ChemDraw document in an ISIS file format for export to an ISIS application, or import a file created by an ISIS application into ChemDraw. ChemDraw Pro provides two File format: ISIS/Sketch (*.skc) for saving files as a binary sketch file for transfer to another ISIS application running under Windows or Macintosh (this is the format used on the Clipboard as well); ISIS/TGF (*.tgf) for saving as an ASCII text file (a Transportable Graphics File) for transfer to ISIS applications on other platforms.

NOTE: When transferring between ChemDraw and ISIS/Draw, if information in a file or on the Clipboard contains only non-bond, unsupported objects, the information is imported as a WMF (metafile) or PICT graphic. However, if a supported object, such as a bond, is also in the file or on the Clipboard, then only the supported object appears.

NOTE: Object types in ISIS not supported in ChemDraw, such as polygons, are not transferred. Object types in ChemDraw not supported in ISIS are not transferred. However, in some cases, such as different arrow types, the arrow is converted to the most similar form. If text in an ISIS Superatom matches a Nickname in ChemDraw it is represented in ChemDraw using the Nickname. If the text does not match a Nickname you are alerted and asked to either copy the Superatom as a label without any chemical significance, or to expand the Superatom and paste it as a structure. See "Nicknames" in Chapter 8, Advanced Drawing Techniques.


ISIS/Reactions (*.rxn)

The ISIS/Reactions format, also referred to as RXN is an MDL-developed format for storing chemical reaction information, used by the ISIS family of products among others.

For single step single or multi-line reactions, ChemDraw uses the point of the reaction arrow as the dividing line to determine which molecules in a reaction are reactants and which are products. Molecules whose centers are behind and/or above the tip of the arrow are considered reactants, and all remaining molecules are products. The reaction arrow can be at any orientation, i.e., it does not have to be parallel to the x-axis. If a reaction contains multiple arrows, then the largest arrow is used as the reaction arrow

NOTE: Reactions with intermediate step (multi-steps) cannot be saved using the RXN file format.

NOTE: ChemDraw will only recognize structures. Symbols, such as "+", will be ignored.

Reaction mapping and reaction center information is stored in the rxn output file.


MDL MolFile (*.mol)

Molecular Design Limited MolFile (MDL MolFile) file format is used by several other Windows, Macintosh and UNIX chemical databases and drawing applications such as ISIS/Drawª, ISIS/Baseª, MACCSª, and REACCSª. There are two MDL MolFile formats provided in ChemDraw Pro: MDL MolFile (Text) and MDL MolFile (Mac). MDL MolFile files are ASCII text files that can be created or edited in common word processing applications or text editors. Atom and bond property information is stored in the molfile.


Molecular Simulations MolFile (*.msm)

Molecular Simulations MolFile format is an ASCII text file used by applications such as ChemNote (tm). You can save a ChemDraw Pro document in Molecular Simulations MolFile format for export to one of these applications.

NOTE: ChemDraw version 4.0 uses the file extension ".msm" for Molecular Simulations MolFiles rather than the standard ".mol", used by Molecular Simulation, Inc. ChemDraw recognizes files with the ".mol" file extension as MDL MolFiles. In addition, the extension ".msi " used in earlier versions of ChemDraw is no longer recognized in ChemDraw 4.5. To open Molecular Simulations MolFiles that have a ".mol" or ".msi " extension you must first change the extension to ".msm".


PICT (Macintosh)

PICT files contain a QuickDraw representation of a ChemDraw picture that can be used by various drawing applications. You can save a ChemDraw document in the PICT format so it can be opened by one of these other applications. The PICT file format contains ChemDraw structural information. PICT files created by ChemDraw version 4.0 or earlier can be reopened and edited by ChemDraw version 4.0. PICT files created by ChemDraw 4.5 can be edited by ChemDraw 3.x, but not by earlier versions of ChemDraw.

All colors are saved in the PICT file except for the Background color.


PICT scaled 4X (Macintosh)

PICT scaled 4x files are the same as PICT files, except that the drawing is four times larger. When these larger files are placed into certain other applications and shrunk back down to 1Ú4 size, they may provide higher quality output than regular PICT files.


SMD

Standard Molecular Data (SMD) file format, version 4.3, is an ASCII text file commonly used by programs that search Chemical Abstracts Databases such as STN Express (tm). You can save your ChemDraw document in SMD format and use the file for searching in a Chemical Abstracts database.


Template Style Sheet (*.cts)

The Template Style Sheet file format is used for saving document settings and row and column characteristics for creating ChemDraw Template documents.


Windows Metafile (Windows Only) (*.bmp)

The Windows Metafile file format saves the GDI representation of a ChemDraw picture. Using the WMF file format you can transfer ChemDraw pictures to other applications, such as Word for Window, that support that WMF file format on the same or different computers rather than using the Clipboard. The WMF file format contains ChemDraw structural information. WMF files created by ChemDraw version 4.0 or earlier can be reopened and edited by ChemDraw version 4.0. WMF files created by ChemDraw 4.5 can be edited by ChemDraw 3.x.


TIFF
TIFF (*.tif)

TIFF format (Tagged Image File Format) is a high resolution format commonly used for saving graphics for importing into desktop publishing applications on the same or on different computer platforms. TIF images can be saved using a variety of resolution, color and compression options. As TIF images can get rather large, choosing appropriate options is important. The TIFF format is for export only.

Resolution

Available resolutions range from 72 (computer monitor) and 1440 dpi (high resolution output). When choosing a resolution, keep in mind that the size of the file increase as the square of the resolution.

Color

Monochrome: forces all objects to black and white.

RGB Indexed: Stores colors using computer monitor style of color encoding.

CMYK Planar: Uses printing press style of color encoding. Groups each color type sequentially. This provides better compression, i.e. CCCCCCMMMMMMYYYYYYKKKKK rather than CMYKCMYKCMYKCMYK, This mode produces far better compression via the PackBits compression method. However, many desktop publishing packages do not support CMYK Planar files.

CMYK Contiguous: Uses printing press style of color encoding. Stores colors non-sequentially i.e. CMYKCMYK. The PackBits compression type will provide no compression for this type of file.

NOTE: Black and white images will be saved as black and white regardless of the options that you set. In addition, images that are imported from other applications will not print black and white unless you set the Color option to Monochrome.

Compression

PackBits: .this compression type reduces files size by encoding repeating bytes of information as output when using the CMYK Planar color option. Below is a highly simplified representation of this compression scheme: for a line of color information such as CCCCCMMMMMYYYYYKKKKK the compression will yield a smaller file by representing the information as C46M5Y5K.

CCITT Group 3: compression type used for fax transmissions of images.

CCITT Group 4: another compression type used for fax transmissions of images.

Deflate: A compression type similar to LZW compression. Works well with all Color and Resolution options.

To set these options, click the Options button in the Save dialog box after you have chosen the TIFF file format.

NOTE: In the Macintosh version you may want to increase the memory allocated to ChemDraw if you are saving large TIFF files.

Once you change the options you must quit ChemDraw and restart in order for the changes to take effect.


PNG

PNG (Portable Network Graphics) format is an alternative to the GIF format for adding graphics to web pages. You can save, but not open, files in PNG format. The PNG format is fairly new and was designed to address many of the shortcomings of the GIF format. In particular, the PNG file format offers true color images, is less prone to transmission errors and offers a full alpha channel for specifying background or transparency options.

For additional information about PNG visit : http://www.boutell.com/boutell/png or http://www.wco.com/~png/


Appendix A, The Chemistry of ChemDraw - Overview
Overview

As you work, ChemDraw automatically converts your various lines, characters, and other symbols into chemically meaningful figures. Normally, much of this work is silent, but you can choose to view this chemical data using the Check Structure, Analyze Structure, and Expand Atom Labels commands. ChemDraw also uses this chemical data when exporting to file formats that support only a subset of the notations that ChemDraw does.

This appendix illustrates how ChemDraw uses its chemical intelligence to interpret what you have drawn. It also shows some of the ways you can help ChemDraw better understand what you mean. Also discussed are a few cases where ChemDraw might not understand what you think is a perfectly reasonable diagram.


Is all of this really necessary?

In a word, no. ChemDraw was designed as a tool to aid in chemical communication, but it is a tool only. Walk up to any chemist and say "benzene," and both of you will immediately understand what substance is being discussed. Similarly will you be understood if you draw a six-membered ring of alternating single and double bonds, regardless of the size, color, orientation, or thickness of the ring itself — and regardless of what ChemDraw thinks about it.

Still, just because it is not necessary does not mean it is not useful. If you're investigating organic acids, a compound with the structural formula CH3COO would most probably represent acetic acid; present the same formula in a paper on transition metal chemistry, and you might be describing a novel methylated cobalt oxide. If you had asked ChemDraw what it thought beforehand, you would have received a message reporting a valence error, and you might have been prompted either to add a negative charge or to change the capitalization.

In this way ChemDraw's chemical intelligence can be used as a sophisticated "spelling" checker for chemical compounds.

It is important to remember that chemists are generally a whole lot smarter than computers. Most chemists would understand AcOo-C6H4COOH immediately, whether or not they recognized it as aspirin. Most computer programs, however, require what is known as a "complete connection table," in this case a collection of 21 atoms connected by 5 double bonds and 16 single bonds in a specific pattern. With its chemical intelligence, ChemDraw can take what makes sense to you as a chemist, and convert it into what makes sense to another application.

More:

There are conventions, and there are conventions...

But that's not what I meant!


There are conventions, and there are conventions...

Unfortunately, making sense is only half the battle when searching chemical databases. Most databases require not only that you draw a structure in a way that makes sense, but that you draw it in the way that they expect. Consider ferrocene, which is represented in at least four different ways in major databases:

Figure A-1 Ferrocene

		and 3 other isomers
Merck Index		Beilstein
Aldrich		MDL ACD
A successful search in one database might produce absolutely no hits in another. When in doubt, consult the documentation for your database, and see if it offers any clues to the conventions used.


But that's not what I meant!

ChemDraw can offer only suggestions, and when it comes down to it, ChemDraw's suggestions don't matter. If you and your audience both understand what you are trying to depict, then you should rightly ignore ChemDraw's complaints. In many cases you can silence ChemDraw permanently by teaching it to understand the notation you're using. For more information, see "Nicknames" in Chapter 8, Advanced Drawing Techniques.


Chemistry In ChemDraw

The remainder of this chapter focuses on the chemical conventions understood by ChemDraw.

More:

Bonds

Atom Labels

Chemically-significant Text

Charges

Isotopes

Radicals

H-Dot/H-Dash

Complexes

Multi-center Attachments

Stereochemical Flags

Query Properties

Analysis Messages


Bonds

Table A-1 Types of bonds

	Single bond, unspecified stereochemistry.
	Single bond, "down" stereochemistry (into the plane of the paper, away from the viewer), from the first drawn atom to the second drawn atom.
	Single bond, "up" stereochemistry (out of the plane of the paper, toward the viewer), from the first drawn atom to the second drawn atom.
	Single bond, mixture of "up" and "down" stereochemistries in some unspecified proportion.
	Dative bond. Often used to indicate polar bonds in N-oxides, for example.
	Double bond, with cis/trans stereochemistry as drawn.
	Double bond, with cis/trans stereochemistry unknown.
	Tautomeric bond, either single or double according to rules of tautomerism.
	Aromatic bond, part of a delocalized resonance system.
	Triple bond.
In addition, a single bond near a closed circle will be recognized as aromatic:

Figure A-2


Appendix A, The Chemistry of ChemDraw - Chemistry In ChemDraw - Atom Labels
Atom Labels

A simple atom label may contain any of the following:

Table A-2 Types of atom labels

	A single element.
	An element and some number of hydrogens.
	A nickname.
	Repeating units within parentheses.
	A series of any combination of the above.
When analyzing an atom label, ChemDraw generally starts at the left and continues to the right, applying standard rules of valence to determine which atoms are bound to which. The exception is with an atom label in Automatic alignment on the left side of a compound. This sort of atom label is displayed "backwards" (H3CO instead OCH3) and is therefore parsed from right to left. Standard valences for each atom are defined in the Isotopes Table (Macintosh) or isotopes.txt (Windows).

By definition, a "simple" atom label has all bonds attached to the first (or last) character. A multi-attached atom label has bonds connected to more than one character, or has all of its bonds attached to a specific character in the middle of the atom label. Multi-attached atom labels are always parsed from beginning to end, but again the beginning might be on the right if the atom label was in Automatic style and on the left side of the original structure:

Table A-3 Types of multi-attached atom labels

	A multi-attached label that is parsed from left to right.
	A multi-attached label that is parsed from right to left.
	A bond attached to the open parenthesis of a repeating group is treated as if bonded to the first of those groups.
	A bond attached to the close parenthesis or repeat count of a repeating group is treated as if bonded to the last of those groups.


Chemically-significant Text

Often it is simpler to write a chemical formula like MeOH or H2O than it is to draw out an entire atoms-and-bonds structure. ChemDraw will correctly interpret any unambiguous structural formula. In this way, CH3COCH2CH3 is recognized as methyl ethyl ketone; MeOH is recognized as methanol. On the other hand, C6H6 might mean benzene, or it might mean one of over 200 other isomers. C6H6 is not recognized by ChemDraw, and will generate an error message if you try to analyze it. Generally, empirical formulas (C2H6 and H2SO4) are not recognized, but structural formulas (CH3CH3 and HOSO2OH) are.

Chemically-significant text must be entirely in Formula or (for isotopes and charges) Superscript style. ChemDraw will not recognize a chemical formula embedded within a larger block of text.

Table A-4 Examples of chemically-significant text

	If you draw a bond, add an atom label, then delete the bond, you have a chemically meaningful text block whose font, size, and style match other atom labels.
	If you create a caption with the text tool and set it to Formula style, you have a chemically meaningful text block whose font, size, and style match other captions.


Appendix A, The Chemistry of ChemDraw - Chemistry In ChemDraw - Charges
Charges

Charges may be created as part of a textual atom label or with the appropriate symbol from the Chemical Symbols Palette. Charges are always assigned to a specific element in the atom label, whose acceptable valences become those of the similar isoelectronic neutral element.

Table A-5 Examples of charges

	A charge following an element is assigned to that element.
	A charge that does not follow an element is assigned to the next element.
	Charges that follow a monovalent element with a repeat count are assigned to the element before that element.
	Charges that follow other repeating units are distributed among those units.
	Charges may be superscripted.
	Multiple charges are recognized appropriately.
	Charges may have repeat counts as long as both the charge and the repeat count are superscripted.
	A "floating" charge placed with the Chemical Symbols Tool is assigned to the nearest atom. (If no atom is within the distance set as the Fixed Length, the charge is ignored and not assigned to any atom).


Appendix A, The Chemistry of ChemDraw - Chemistry In ChemDraw - Isotopes and Elements
Isotopes and Elements

By default, ChemDraw will correctly recognize all isotopes in the full Table of the Elements; this data has been provided by CRC Press, Inc1. Isotopes are defined in the Isotopes Table (Macintosh) or isotopes.txt (Windows). In the extremely unlikely event that you need to modify add new isotopes, this file can be edited with any text editor.

Table A-6 Examples of isotopes

	Isotope numbers are indicated by a superscripted number before the element symbol
	Isotopes can be included anywhere that regular elements can.
	Deuterium and Tritium can be indicated by their one-letter symbols.
1Adapted from the Table of Isotopes data, in the CRC Handbook of Chemistry and Physics, 77th Ed., Lide, D.R., Editor-in-Chief, CRC Press, Boca Raton, Florida, ©1996. With permission.\


Radicals

Radicals are indicated with the appropriate symbol from the Chemical Symbols Palette. As with charges, they are assigned to the nearest atom. Radicals always occupy one free valence, in addition to any charge effects.

Figure A-3 Examples of radicals


H-Dot/H-Dash

H-Dot and H-Dash symbols from the Chemical Symbols Palette indicate the stereochemistry of a single hydrogen atom. These symbols are most commonly used in fused systems.

Figure A-4 Examples of H-Dot/H-Dash


Complexes

Compounds with electron pairs can act as Lewis bases, bonding with Lewis acids that are electron-deficient. Similar behavior can be seen between lone pairs and metals.

The best representation of these types of interaction is with a dative bond from the electron-pair donor to the acceptor. With a plain bond instead of the dative one, ChemDraw would report a valence error. The dative bond more accurately represents the electron donation.

Complexes may also be represented with explicit lone pairs and without any bonds at all.

If you do use a plain bond to indicate a complex, you may wish to set Abnormal Valence to Allowed in the Atom Properties dialog.

Table A-7 Examples of complexes

	Boron trifluoride-ammonia complex.
	Boron trifluoride-acetic acid complex.
	Heme, a compound with two formal covalent bonds and two formal donor-acceptor pairs.
	Another representation of heme.


Multi-center Attachments

Multi-center attachments are meaningful only when created using the Add Multi-Center Attachment command from the File Menu. This command creates a pseudo-atom that is disregarded during chemical calculations, but still allows you to create diagrams that look meaningful to the experienced chemist.

Table A-8 Examples of multi-center attachments

	η3 or π-Allyl complex.
	Ferrocene, a π-Aryl complex.
	Cp2TiCl2, another π-Aryl complex.
	η-C5H5Mn(CO)3


Appendix A, The Chemistry of ChemDraw - Chemistry In ChemDraw - Stereochemical Flags
Stereochemical Flags

While the chirality of a specific stereocenter can be indicated with the appropriate wedged, hashed, or plain bond, sometimes it is useful to indicate the relative stereochemistry of a molecule as a whole, considering the relationship between all stereocenters. Stereochemical flags apply to the nearest structure; if no structure is within the distance specified by the Fixed Length value, the stereochemical flag is not assigned to any structure.

Table A-9 Examples of stereochemical flags

	The Absolute flag indicates the exact stereoisomer as drawn.
	The Relative flag indicates the exact stereoisomer as drawn, or its enantiomer.
	The Racemic flag indicates a mixture of the exact stereoisomer as drawn and its enantiomer.


Query Properties

By their nature, query properties do not represent actual chemical features, but rather describe broad classes or groups of features. For information on using query properties, see Chapter 9, Drawing Query Structures.


Analysis Messages

Occasionally, ChemDraw may be unable to analyze your structure fully for one reason or another. There are two general types of messages: status messages that report a problem that might not affect the final analysis, and critical messages that probably will.

Table A-10 Examples of analysis messages

There are too many bonds to this unlabeled Carbon.	Displayed for every unlabeled atom with more than 4 filled valences. Filled valences include sum of bond orders, charge, radicals, and free sites. Aromatic bonds count 1.5 each, rounded down unless it is the only bond to the atom. Charge is signed and includes charge implied by dative bonds. The Substituents query property treats Free Sites, Up to and Exactly the same way, that is, an atom with 2 explicit bonds and "Substituents: Up To 3" or "Substituents: Exactly 3" or "Substituents: Free Sites 1" has three filled valences.
An atom in this label has an invalid valence.	Displayed in a variety of cases where ChemDraw cannot find a place to put a bond or cannot find a bond to put on an atom. Valid valences for each element are listed in the Isotopes Table (Macintosh) or isotopes.txt (Windows).
ChemDraw can't interpret this label.	Displayed when ChemDraw finds text that it cannot identify as an element, nickname, generic nickname, or alternative group name.
Parentheses don't match.	Displayed when parentheses cannot be matched into nested open-close pairs.
This label has conflicting or unassignable charges.	Displayed when a plus and minus charge have been assigned to the same element, charges have been assigned in more than one way, or a charge has been assigned to a nickname, generic nickname, or Alternative Group name.
An unknown error occurred in the label interpreter.	You should never see this message. If you do, please contact CambridgeSoft Technical Support with information on the label that produced it. See Appendix C, Technical Support, for more information.
ChemDraw can only check odd-membered aromatic rings when drawn with explicit double bonds.	Displayed for every circle in an odd-sized ring. This is a status message only; analysis will continue but may produce inaccurate results.
Formula cannot be computed for queries.	Displayed for every label that contains a generic nickname, an element list or an alternative group. This is a status message only; analysis will continue as if the problematic label were not selected.
Text not in Formula style won't be interpreted.	Displayed for the first caption that is not an atom label or Alternative Group name, and which contains any text not in Formula, Subscript, or Superscript style. This is a status message only, and will appear only once regardless of how many captions are in the selection.
This named alternative group contains no attachment point.	Displayed for any structure within an Alternative Group Box where the structure lacks an attachment point. This is a status message only.
This named alternative group contains fragments with inconsistent valences.	Displayed for any Alternative Group Box whose contained structures have varying numbers of attachment points. Since all structures within an Alternative Group Box are to be used interchangeably, they must have the same number of attachments. This is a status message only.
This named alternative group contains no fragment.	Displayed for any Alternative Group Box that is empty. This is a status message only.
Part of a molecule is outside of the alternative group definition.	Displayed for any Alternative Group Box whose border crosses part of a structure. This is a status message only.


Appendix B, Specifying Paths - Overview
Overview

This appendix describes the path information necessary to locate the cd_items directory under Windows or the ChemDraw Folder on the Macintosh.


Windows:
Windows

Normally, the cd_items directory is in the same directory as the ChemDraw application and the path is automatically set. However, if you want the cd_items folder to reside in a different directory, you must specify the path in the chemdraw.ini file.

When the path is not specified properly, ChemDraw displays an error message and quits.

To change the path in the chemdraw.ini file if you are using Windows:

·	Open the chemdraw.ini file using a text editor, such as the Windows Notepad application found in the Accessories program group.

NOTE: You should always create a backup of the chemdraw.ini file before you make any edits. Use the backup file if for any reason the edited file does not work properly.

Normally, the chemdraw.ini file is located within your Windows directory.

The following is an example of the text that appears:

cd_items_PATH=C:\CHEMDRAW\cd_items WindowPosition=10, 10, 712, 561 PalettePostion=14,52

The path information for the cd_items directory is specified in the line beginning with "cd_items_PATH=". If this line doesn't exist, you should create it, otherwise ChemDraw looks for the cd_items directory in your local directory.

To specify the path (Information within the chemdraw.ini file isn't case sensitive):

·	Type the path after "cd_items_PATH="

For example, if the cd_items directory is located within a directory called "users" on drive C, type:

·	c:\users\cd_items

The complete line would read "cd_items_PATH=c:\users\cd_items"

After specifying the path:

·	Save the changes and close the chemdraw.ini file.

To implement the changes:

·	Exit and restart ChemDraw.


Macintosh:
Macintosh

When ChemDraw 4.5 is installed the ChemDraw Folder is placed in the same folder as the application. However, if you are using ChemDraw from a file server and you want to have your own ChemDraw folder, place the ChemDraw folder in the Preferences folder in your System folder. ChemDraw will always look for the ChemDraw folder in the Preferences folder first, followed by the application folder second.


Appendix C, Technical Support - Overview
Overview

CambridgeSoft Corporation (CS) provides technical support to all registered users of this software through the World Wide Web (WWW), and through our Technical Support department.

Our Technical Support pages on the WWW contain answers to frequently asked questions (FAQs), in addition to some general information about our software. You can access our Technical Support page using the following address:

http://www.camsoft.com/support.html

If you don't find the answers you need on the WWW, please complete the following tasks before contacting the Customer Support Department.

Step 1: Check the Readme file for known limitations or conflicts.

Step 2: Check the system requirements for the software at the beginning of this help file.

Step 3: Read the Troubleshooting section of this appendix and follow the possible resolution tactics outlined there.

Step 4: If all your attempts to resolve a problem fail, fill out a copy of the CS Software Problem Report Form at the back of this help file. This form is also available on-line through our WWW Technical Support page.

·	Try to reproduce the problem before contacting us. If you can reproduce the problem, please record the exact steps that you took to do so.

·	Record the exact wording of any error messages that appear.

·	Finally, please record anything that you have tried to correct the problem.

You can deliver your CS Software Problem Report Form to Technical Support by the following methods:

Internet:	 support@camsoft.com CompuServe: 76070,615 America On-line: CamSoft  Fax: 617 491-7203

Mail:	 	CambridgeSoft Corporation 	ATTN: Technical Support 	875 Massachusetts Avenue 	Cambridge, MA 02139 USA


Serial Numbers

When contacting Technical Support, you must always provide your serial number. This serial number was on the outside of the original ChemDraw box, and is the number that you entered when you launched ChemDraw for the first time. If you have thrown away your box and lost your installation instructions, you can find the serial number in the following ways:

More:

Macintosh

Windows


Macintosh

·With ChemDraw launched, choose About CS ChemDraw from the Apple menu. The serial number will appear at the bottom left of the about box.

·In the Finder, single-click on the ChemDraw application icon and choose Get Info from the File menu. The serial number will be listed immediately after the version.


Windows

·With ChemDraw launched, choose About CS ChemDraw from the Help menu. The serial number will appear at the bottom left of the about box.

·Open the chemdraw.ini file (in your Windows directory) using any text editor. The serial number will appear in the line starting "SERIAL_NO=".


Troubleshooting

This section describes steps you can take that affect the overall performance of ChemDraw, as well as steps to follow if your computer crashes when using a CS software product.

More:

Launching

Performance

System Crashes


Launching

If ChemDraw can't find the ChemDraw Folder (Macintosh) or cd_items directory (Windows) you will not be able to launch the program. See Appendix B, Specifying Paths SpecifyingPathsfor additional information about the appropriate location.


Performance

Below are some ways you can optimize the performance of ChemDraw:

Step 1. Installing the non Power Macintosh version of ChemDraw on a Power Macintosh will likely decrease performance. Step 2 (Macintosh): Increase the total amount of memory that the application can use:

·	Select the ChemDraw application icon in the Finder when ChemDraw is not running.

·	From the Edit menu, choose Get Info. Increase the memory allocation in the Preferred size text box in the Memory Requirements section of the dialog box.

Step 2 (Windows) In the "386 Enhanced" control panel (Windows 3.1, 3.1.1, and Windows for Workgroups), the "System" control panel (Windows NT 3.5.1) or the "Performance" tab in the System control panel (Windows 95 or Windows NT 4.0), allocate more processor time to ChemDraw.

Step 3: Install more physical RAM. The more you have, the less ChemDraw will have to access your hard disk to use Virtual Memory.

Step 4 Increase the Virtual Memory (VM). Virtual memory extends RAM by allowing space on your hard disk to be used as RAM. However, the time for swapping between the application and the hard disk is slower than swapping with physical RAM. Here is where you can change VM:

·	Macintosh: Memory control panel.

NOTE: If you are running a Power Macintosh, the optimum virtual memory setting is one MB greater than the physical RAM. Any changes -either by increasing the virtual memory or by turning it off altogether- will significantly lower performance.

·	Windows 3.1: 386 Enhanced control panel.

·	Windows 95 and Windows NT 4.0: Performance control panel.

·	Windows NT 3.5.1: System control panel.


System Crashes

ChemDraw should never crash, but below are the steps you should go through to try to resolve issues that cause computer crashes while using a CS software product.

Step 1: Restart your computer (Macintosh), or restart Windows. Next, try to reproduce the problem. If the problem does reoccur, keep reading.

Step 2 (Macintosh): Restart your computer while holding the Shift key down to turn off all system extensions. Try to repeat the problem.

If the problem no longer occurs, then you likely have an extension conflict. You should determine which extension is causing the conflict, and then not have it load when using ChemDraw. To isolate an extension, disable half of your extensions using the Extension Manager and test the problem again. Keep disabling half of your extensions until you find which extension(s) are causing the problem. Please inform Technical support which extension(s) is/are causing the problem.

Step 2 (Windows): The most common conflicts for Windows users concern Video Drivers, Printer Drivers and Win32s conflicts (if you are running under Windows 3.1, 3.11 or Windows for Workgroups). If you do end up needing to contact us, be sure to determine what type of drivers you are using and the version of Win32s if you are using Windows 3.1.

Video Driver related problems: If you are having problems with the display of ChemDraw, try switching to the VGA video driver in the display Control Panel (or System Setup then retest the problems. If using a different driver helps, your original driver may need to be updated-contact the maker of the driver and obtain the most up-to-date driver. If you still have trouble contact us with the relevant details about the original driver and the resulting problem.

Printer Driver related problems: Try using a different printer driver. If using a different driver helps, your original driver may need to be updated-contact the maker of the driver and obtain the most up-to-date driver. If you still have trouble contact us with the relevant details about the original driver and the resulting problem.

Win32s related problems: For Windows 3.1, 3.11 and Windows for Workgroups users, make sure you have the latest version of Win32s. This can be downloaded from Microsoft's WWW or FTP sites.

Step 3 (All): Try reinstalling the software. For users of Windows 3.1, Windows 3.11 or Windows for Workgroups you must uninstall the software before reinstalling. See the complete uninstall instructions on the Technical Support page on the WWW.

Step 4: If the problem still occurs, Fax or Email the details of the problem to customer support.


Appendix D, Document Settings - Overview
Overview

This Appendix contains a table of drawing setting and an example structure for each of the Style Sheets/ Stationery Pads shipped with ChemDraw.

Creating your own Style Sheets/Stationery Pads is easy. Simply create a new document, enter the settings in the Page Setup, Drawing, Text Settings and Color Palette dialog box and choose Save Stationary/Style Sheet from the File menu. In the dialog box, make sure the ChemDraw Style Sheet (Windows) or ChemDraw Stationery (Macintosh) file format is selected, type a name for the document, choose the location for saving as cd_items directory (Windows) or ChemDraw Folder (Macintosh) and click the OK button (Windows) or Save button (Macintosh).

Table D-1 Drawing and Text (atom label and caption) Settings in Journal Style Sheets/Stationery Pads

	ACS-1996 Fixed Length: 14.4 pt  Bold Width: 2 pt  Line Width: 0.6 pt  Margin Width: 1.6 pt  Hash Spacing: 2.5 pt  Chain Angle (degrees): 120  Bond Width (% of length): 18  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 10 pt  Caption Font (Win/Mac): Arial/Helvetica  Caption Size: 10 pt  Drawing Area (Width x Height): 540 pt x 720 pt  Page Size: US Letter  Reduction (%): 100
	Can. J. Chem Fixed Length: 18 pt  Bold Width: 2.5 pt  Line Width: 0.8 pt  Margin Width: 2 pt  Hash Spacing: 3 pt  Chain Angle (degrees): 120  Bond Width (% of length): 18  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 12 pt  Caption Font (Win/Mac): Arial/Helvetica  Caption Size: 12 pt  Drawing Area (Width x Height): 540 pt x 720 pt  Page Size: US Letter  Reduction (%): 80
	J. Mol. Mod. Fixed Length: 14.4 pt  Bold Width: 2 pt  Line Width: 0.6 pt  Margin Width: 1.6 pt  Hash Spacing: 2.5 pt  Chain Angle (degrees): 120  Bond Width (% of length): 18  Atom Label Font (Win/Mac): Times New Roman/Times  Atom Label Size: 10 pt  Caption Font (Win/Mac): Times New Roman/Times  Caption Size: 10 pt  Drawing Area (Width x Height): 8.5 cm x 25.4 cm (1 column)  17 cm x 25.4 cm (2 column)  Page Size: US Letter  Reduction (%): 100
	RSC-1995 Fixed Length: 0.7 cm  Bold Width: 0.092 cm  Line Width: 0.025 cm  Margin Width: 0.071 cm  Hash Spacing: 0.099 cm  Chain Angle (degrees): 120  Bond Width (% of length): 20  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 12 pt  Caption Font (Win/Mac): Arial/Helvetica  Caption Size: 12 pt  Drawing Area (Width x Height): 19.05 cm x 25.4 cm  Page Size: US Letter  Reduction (%): 60
	Synthesis/SYNLETT Fixed Length: 17 pt  Bold Width: 2 pt  Line Width: 0.8 pt  Margin Width: 1.3 pt  Hash Spacing: 2.5 pt  Chain Angle (degrees): 120  Bond Width (% of length): 18  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 10 pt  Caption Font (Win/Mac): Arial/Helvetica  Caption Size: 10 pt  Drawing Area (Width x Height): 12 cm x 26.7 cm  Page Size: A4  Reduction (%): 100
	New Document Fixed Length: 30 pt  Bold Width: 2 pt  Line Width: 1 pt  Margin Width: 2 pt  Hash Spacing: 2.7 pt  Chain Angle (degrees): 120  Bond Width (% of length): 12  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 10 pt  Caption Font (Win/Mac): Times New Roman/Times  Caption Size: 12 pt  Drawing Area (Width x Height): 7.5 in x 10 in  Page Size: US Letter  Reduction (%): 100
	New Slide Fixed Length: 30 pt  Bold Width: 4 pt  Line Width: 1.6 pt  Margin Width: 2 pt  Hash Spacing: 2.7 pt  Chain Angle (degrees): 120  Bond Width (% of length): 15  Atom Label Font (Win/Mac): Arial/Helvetica  Atom Label Size: 12 pt  Caption Font (Win/Mac): Times New Roman/Times  Caption Size: 16 pt  Drawing Area (Width x Height): 7.5 in x 10 in  Page Size: US Letter  Reduction (%): 100


Appendix E, Apple Events (Macintosh) - Overview
Overview

ChemDraw supports Apple Events (tm), a method by which applications can send messages to each other. Using Apple Events it is possible to develop scripts for sequences of commands that can be executed repeatedly.

ChemDraw supports the Required Suite, a basic set of Apple Events that includes the Apple Events required to open and print documents from the Macintosh Finder.

 ChemDraw supports the menu sharing Apple Events used in conjunction with Frontier, by Userland, Inc. Using Frontier, you can add items to the menu bar of ChemDraw that execute Frontier scripts.

For a complete technical specification of the Apple Events that ChemDraw supports, drag the ChemDraw application icon onto the Script Editor application icon or choose Open Dictionary from the Script Editor's File menu.


Appendix F, Chemistry File Formats - Overview
Overview

Using the file interpreters provided with ChemDraw you can open documents saved in other file formats. This appendix discusses the following file interpreters that are provided with ChemDraw and ChemDraw Pro.


Example of Other File Formats

The following are more detailed descriptions of the MDL MolFile , Connection Table, ISIS, SMD and Molecular Simulations MolFile file formats supported by ChemDraw.

The following example format files were generated using ChemDraw. This is the same information that is interpreted when the file is generated by another application in the particular format and opened using the appropriate ChemDraw file interpreter/format.

There are several generalizations about the files that apply to all format types that are created when you use ChemDraw:

1.Only the atoms that are drawn in the structures are present in the format file.

2.No information is assumed about the structure, for example, valences for atoms are not automatically filled, and atom labels are treated as a single atom.

NOTE: If you are transferring the file to another application, you may find that the application cannot interpret an atom label such as OH or OCH3 and therefore may be unable to interpret the file. When ChemDraw 3.5 creates a file, it expands labels so that each atom in the label has the same coordinates in the resulting output file. There are other applications such as CS Chem3D that can interpret atom labels such as these. You should refer to the documentation for the application you are planning to use to interpret your file to determine if you can use structures with multi-character atom labels, or if you need to expand the atom label so that each atom is represented by an individual atom label.

2.The file formats presented here are all in ASCII (text-only) format, with the exception of ISIS/SKC and MDL Molfile (MAC), and can be created or edited using a text editor.

All format files described in this section are generated for the cyclohexanol structure shown below. All references to atom serial numbers are based on the numbering shown.

Cyclohexanol

More:

Connection Table

 ISIS/Sketch

 Molecular Design Limited MolFiles

 Molecular Simulations MolFile

ISIS/Reactions (*.rxn)

 Standard Molecular Data File


Connection Table

The following is a sample Connection Table file produced using ChemDraw for cyclohexanol (the line numbers are added for purposes of discussion only):

Line 1	Cyclohexanol
Line 2	7 7
Line 3	0.0000	0.5000	0.0000	C
Line 4	-0.8667	0.0000	0.0000	C
Line 5	-0.8667	-1.0000	0.0000	C
Line 6	0.0000	-1.5000	0.0000	C
Line 7	0.8667	-1.0000	0.0000	C
Line 8	0.8667	0.0000	0.0000	C
Line 9	0.0000	1.5000	0.0000	O
Line 10	1 2 1 1
Line 11	2 3 1 1
Line 12	3 4 1 1
Line 13	4 5 1 1
Line 14	5 6 1 1
Line 15	1 6 1 1
Line 16	6 7 1 1
A File in Connection Table Format for Cyclohexanol

Each line represents a data record containing one or more fields of information about the structure. Individual fields are delimited by space(s) or a tab. The fields in the Connection Table format file used by ChemDraw are discussed below. The field value for Carbon 6 from the example file is included in parentheses for reference.

1.	Line 1 is the molecule name. The molecule name is the file name when the file was created using ChemDraw.

2.	Line 2 contains two fields: the first field is the number of atom labels, and the second field is the number of bonds.

3.	Lines 3-9 each contains 4 fields describing information about the individual atoms: the first field is the X Cartesian coordinate (0.8667), the second field is the Y Cartesian coordinate (0.0000), the third field is the Z Cartesian coordinate (0.0000), and the fourth field is the atom label (C).

4.	Lines 10-16 each contains four fields describing information about the individual bonds between the atoms: the first two fields represent the serial numbers of the atoms that are connected by this bond (atom 1 and atom 6), the third field is the bond order (1) and the fourth field is the bond type (1).

The bond types for the Connection Table format are as follows:

Single Bonds

1	Solid

2	Dashed

3	Hashed

4	Wedged hash with first atom at narrow end

5	Wedged hash with second atom at narrow end

6	Bold

7	Wedged with first atom at narrow end

8	Wedged with second atom at narrow end

9	Wavy

10	Hollow wedge with narrow end towards 1st atom

11	Hollow wedge with narrow end towards 2nd atom

12	Dative bond with arrow towards 2nd atom

13	Dative bond with arrow towards 1st atom

14	Any (bond property)

15	Single/Double (bond property)

16	Double/Aromatic (bond property)

17	Single/Aromatic (bond property)

Double Bonds (double bonds are numbered based upon bond type and position. Below are some possible numbers for each type. Contact technical support if you want a more detailed file format description).

Plain: 1, 2, 8, 9, 10

Dashed: 6, 12, 13, 14

Bold: 18, 24, 25, 26

Crossed: 34, 40, 41, 42

Double Dashed: 66, 72, 73, 74

Triple Bonds

1 (plain only)


ISIS/Sketch

The ISIS/Sketch file formats are created by Molecular Design Limited for opening and saving files in the format used by ISIS applications. The TGF format is an ASCII format, and therefore it is transportable between platforms. The SKC format is platform specific. TGF files can be created or edited in common word processor. The file below is an example TGF file created with ChemDraw for Cyclohexanol. The Line number are added for illustrative purposes only.

Line 1	$Version:	2
Line 2	$Totobjs:	15
Line 3	$Font: "Helvetica"	100	0
Line 4	$Name:	"c.1.tgf"
Line 5	$Obj: atom
Line 6	$Atom_coords:	2330	2690
Line 7	$Obj: atom
Line 8	$Atom_coords:	2330	2990
Line 9	$Obj: atom
Line 10	$Atom_coords:	2590	3140
Line 11	$Obj: atom
Line 12	$Atom_coords:	2850	2990
Line 13	$Obj: atom
Line 14	$Atom_coords:	2850	2690
Line 15	$Obj: atom
Line 16	$Atom_coords:	2590	2540
Line 17	$Obj: atom
Line 18	$Atom_coords:	2590	2240
Line 19	$Font: "Helvetica"	100	0
Line 20	$Atom_alias: "OH"
Line 21	$Atom_type:	8
Line 22	$Obj: bond
Line 23	$Bond_atoms:	0	1
Line 24	$Obj: bond
Line 25	$Bond_atoms:	1	2
Line 26	$Obj: bond
Line 27	$Bond_atoms:	2	3
Line 28	$Obj: bond
Line 29	$Bond_atoms:	3	4
Line 30	$Obj: bond
Line 31	$Bond_atoms:	4	5
Line 32	$Obj: bond
Line 33	$Bond_atoms:	0	5
Line 34	$Obj: bond
Line 35	$Bond_atoms:	5	6
Line 36	$EndSketch:

Each line represents either a blank line, or a data record containing one or more fields of information about the structure. Each field is delimited by spaces. The records in the ISIS/Sketch (.TGF) format file used by ChemDraw Pro are discussed below.

1. Line 1 contains version for the ISIS/Sketch file format.

2. Line 2 contains the total number of objects, this includes 1 object for each atom coordinate, atom alias, and bond.

3. Line 3 contains the name of the font(s) used for atoms.

4. Line 4 contains the name of the file containing the structure.

5. Line 5-18 (in this example) include the X and Y coordinates for the atoms in cyclohexane. Each coordinate is preceded by a section delimiter "$Obj.atom" indicating that a coordinate follows.

6. Line 19 contains the font information for atom aliases in the structure.

7. Line 20 contains information about atom aliases in the structure In this example "OH".

8. Line 21 contains information about the atom types in the structure.

9. Line 22-35 contains information about the bonds between the atoms in the structure. Each record is preceded by a section delimiter "$Bond.atom" indicating that a bond table follows.


Molecular Design Limited MolFiles

The Molecular Design Limited MolFile (MDL MolFile ) format is defined in the Journal of Chemical Information and Computer Science, Volume 32, Number 3, 1992, pages 244-245.

MDL MolFiles can be created or edited in common word processing applications.

The following is a sample MDL MolFile file produced using ChemDraw Pro for cyclohexanol (the line numbers are added for purposes of discussion only).

Line 1	cyclohexanol
Line 2
Line 3
Line 4	7 7 0 0 0
Line 5	-1.2972	0.5000	0.0000	C	0 0 0 0 0
Line 6	-1.2972	-0.5000	0.0000	C	0 0 0 0 0
Line 7	-0.4305	-1.0000	0.0000	C	0 0 0 0 0
Line 8	0.4361	-0.5000	0.0000	C	0 0 0 0 0
Line 9	0.4361	0.5000	0.0000	C	0 0 0 0 0
Line 10	-0.4305	1.0000	0.0000	C	0 0 0 0 0
Line 11	1.3000	1.0000	0.0000	O	0 0 0 0 0
Line 12	1 2 1 0 0 0
Line 13	2 3 1 0 0 0
Line 14	3 4 1 0 0 0
Line 15	4 5 1 0 0 0
Line 16	5 6 1 0 0 0
Line 17	1 6 1 0 0 0
Line 18	6 7 1 0 0 0
A File in MDL MolFile Format for Cyclohexanol

Each line represents either a blank line, or a data record containing one or more fields of information about the structure. Each field is delimited by space(s) or a tab. The fields in the MDL MolFile format file used by ChemDraw Pro are discussed below. The field value for Carbon 6 from the example file is included in parentheses for reference.

1.	Line 1 contains the name of the molecule. The molecule name is the file name when the file was created using ChemDraw Pro.

2.	Lines 2 and 3 are blank lines and are ignored.

3.	Line 4 contains 5 fields describing information about the molecule: The first field is number of atoms (7), the second field is the number of bonds (7), the third field is the number of atom lists (0), the fourth field is not used (0), the fifth field indicates stereochemistry (0). ChemDraw Pro ignores the number of atom lists, the unused field and stereochemistry. These fields will always contain a zero if the file was created using ChemDraw Pro.

4.	Lines 5-11 each contain 9 fields describing information about the atoms in the structure: The first field is the X coordinate (-0.4305), the second field is the Y coordinate (1.0000), the third field is the Z coordinate (0.0000), the fourth field is the atom label (C), the fifth field is the mass difference, the sixth field is the charge (0), the seventh field is the stereo parity designator (0), the eighth field is the number of hydrogens (0), and the ninth field is the center (0).

5.	Lines 12-18 each contain 6 fields describing information about the bonds between the atoms in the structure: the first two fields represent the serial numbers of the atoms that are connected by this bond (atom 1 and atom 6), the third field is the bond order (1), the fourth field is the bond stereo designator (0), the fifth field is not used (0) and the sixth field is the topology code (0).


Molecular Simulations MolFile

The Molecular Simulations MolFileis defined in Chapter 4, "ChemNote File Format" in the Centrum: ChemNote Application documentation, pages 4-1 to 4-5.

NOTE: ChemDraw version 3.5 uses the file extension ".msm" for Molecular Simulations MolFiles rather than the standard ".mol", used by Molecular Simulation, Inc. ChemDraw recognizes files with the ".mol" file extension as MDL MolFiles. In addition, the extension ".msi " used in earlier versions of ChemDraw, is no longer recognized in ChemDraw 3.5. To open Molecular Simulations MolFiles that have a ".mol" or ".msi " extension you must first change the extension to ".msm".

The following is a sample Molecular Simulations MolFile file produced using ChemDraw Pro for cyclohexanol (the line numbers are added for purposes of discussion only):

Line 1	! Polygen 133
Line 2	ChemNote molecular file created by ChemDraw Pro (tm)
Line 3	* File format version number
Line 4	90.0928
Line 5	* File update version number
Line 6	92.0319
Line 7	*
Line 8	* molecule name
Line 9	Undefined Name
Line 10	* empirical formula
Line 11	Undefined Empirical Formula
Line 12	* need 3D conversion?
Line 13	1
Line 14	* 3D displacement vector
Line 15	0.000 0.000 0.000
Line 16	* 3D rotation matrix
Line 17	1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000
Line 18	* 3D scale factor
Line 19	0.000000
Line 20	* 2D scale factor
Line 21	1.000000
Line 22	* 2D attributes
Line 23	1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Line 24	* 3D attributes
Line 25	0 0 0 0 0 0 0 0 0 0 0
Line 26	* Global display attributes
Line 27	1 0 1 12 256
Line 28	* Atom List
Line 29	* Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS sat dfoxid useroxid Sh_type Sh_nr Qstring
Line 30	1 C 255 4168 4680
Line 31	2 C 255 4168 5040
Line 32	3 C 255 4480 5220
Line 33	4 C 255 4792 5040
Line 34	5 C 255 4792 4680
Line 35	6 C 255 4480 4500
Line 36	7 O 255 4480 4140
Line 37	* Bond List
Line 38	* Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qstereo
Line 39	1 1 1 2
Line 40	2 1 2 3
Line 41	3 1 3 4
Line 42	4 1 4 5
Line 43	5 1 5 6
Line 44	6 1 1 6
Line 45	7 1 6 7
Line 46	* Fragment List
Line 47	* Fgmt# Label Atoms
Line 48	* Bond Angles
Line 49	* bond1 bond2 angle locked
Line 50	* Dihedral Angles
Line 51	* at1-cons at1 at2 at2-cons angle locked
Line 52	* Planarity data
Line 53	* User data area
Line 54	* End of File
A File in Molecular Simulations MolFile Format for Cyclohexanol

The Molecular Simulations MolFile format is broken up into several sections. Section headers are preceded by a "*". Blank lines also contain a "*". Each line represents either a blank line, a header line or a data record containing one or more fields of information about the structure. Individual fields are delimited by space(s) or a tab. The fields in the Molecular Simulations MolFile format file used by ChemDraw Pro are discussed below. The field value for Carbon 6 from the example file is included in parentheses for reference:

1.	Line 1 is a standard header line for Molecular Simulations MolFile format files.

2.	Line 2 indicates the application which created the file ChemNote application file format.

3.	Line 3 is the header for the File format version number section.

4.	Line 4 indicates the file format version number. The format for this field is YY.MMDD.

5.	Line 5 is the header for the File update version number section.

6.	Line 6 indicates the file update version number. The format for this field is YY.MMDD.

7.	Line 7 is a blank line.

8.	Line 8 is the header for the molecule name section.

9.	Line 9 contains the field molecule name. This field contains either the file name, or "Undefined Name".

10. Line 10 is the header for the empirical formula.

11. Line 11 contains the empirical formula field. This field contains either the empirical formula or "Undefined Empirical Formula".

12. Lines 12-25 each contains information concerning conversions from 3D to 2D. This information remains constant (as shown) when the file is created using ChemDraw Pro.

13: Line 26 is the header for the Global display attributes section.

14: Line 27 contains 5 fields describing the global display attributes: Line thickness (1), font style (0), type face (1), type size (12), font (256).

NOTE: These values are specific to the platform that is generating the file.

15. Line 28 contains the header for the Atom Lists section.

16. Line 29 contains a listing of all the possible fields for the atom list section. When the file is created using ChemDraw Pro only Atom#, Lbl, Type, x and y are used.

17. Lines 30-36 each contain 5 fields describing information about the atoms in the 2D structure: the first field is the atom number (6), the second field is the atom label (C), the third field is the atom type (255), the fourth field is the Internal X coordinate (4480) and the fifth field is the internal Y coordinate (4500).

NOTE: Atom type is a field used during 3D conversion. A value of 255 (=Not Yet Set) is seen when the file is created using ChemDraw Pro.

18. Line 37 contains the header for the Bond List section.

19. Line 38 contains a listing of all the possible fields for the bond list section. When the file is created using ChemDraw Pro, only Bond #, Bond_typed, atom 1, and atom 2 are used.

20. Lines 39-45 each contain 4 fields describing information about each of the bonds in the structure: the first field is the internal bond number (6), the second field is the bond type (1), the third and fourth fields are the atom serial numbers for the atoms involved in the bond [atom 1 (1), atom 2(6)].

21. Line 46-52 are section headers for 3D conversion use. This section contains the header names only (as shown) when the file is created using ChemDraw Pro.

22. Line 53 is a header for the section User data area. This section contains the header name only (as shown) when the file is created using ChemDraw Pro.

23. Line 54 is a the header that indicates the End of File.


ISIS/Reactions (*.rxn)

The ISIS/Reactions format, also referred to as RXN is an MDL-developed format for storing chemical reaction information, used by the ISIS family of products among others.

NOTE: ChemDraw will only recognize structures. Symbols, such as "+", will be ignored.

Format of a RXNfile:

where rrr and ppp represent the number of reactants and products, respectively. The reactant MOLfile format (*r) and product MOLfile format (*p) are repeated for each reactant and product, respectively. For detailed information regarding the Header Block, see the aforementioned reference.

NOTE: To determine which molecules in a reaction are reactants and which are products, ChemDraw uses the point of the reaction arrow as the dividing line. Molecules whose centers are to the left of the arrow tip are considered reactants, and all remaining molecules are products. The reaction arrow can be at any orientation, i.e., it does not have to be parallel to the x-axis. If a reaction contains multiple arrows, then the largest arrow is used as the reaction arrow.

The RXNfile shown corresponds to the reaction below:

$RXN

 ChemDraw 0718961544

 2 2

$MOL

 ChemDraw 07189615442D

 7 7 0 0 0 0 0 0 0 0 1

 -1.0000 -5.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.5000 -6.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 0.5000 -6.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.0000 -5.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 0.5000 -5.0883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.5000 -5.0883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.7650 6.8200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

 1 2 1 0 0 0 0

 2 3 1 0 0 0 0

 3 4 1 0 0 0 0

 4 5 1 0 0 0 0

 5 6 1 0 0 0 0

 1 6 1 0 0 0 0

 4 7 2 0 0 0 0

M END

$MOL

 ChemDraw 07189615442D

 20 22 0 0 0 0 0 0 0 0 1

 -4.8100 7.4117 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0

 -4.8100 7.4117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.0783 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 2.8117 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.9450 -5.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.0783 -5.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.0783 -6.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1.9450 -7.4117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 2.8100 -6.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 2.8100 -5.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 3.3117 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 4.3117 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 4.8117 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 4.3117 -4.0433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 3.3117 -4.0433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 0.5783 -4.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.4233 -4.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.9250 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -0.4233 -5.7767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 0.5783 -5.7767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1 2 2 0 0 0 0

 1 3 1 0 0 0 0

 1 4 1 0 0 0 0

 1 5 1 0 0 0 0

 5 6 2 0 0 0 0

 6 7 1 0 0 0 0

 7 8 2 0 0 0 0

 8 9 1 0 0 0 0

 9 10 2 0 0 0 0

 5 10 1 0 0 0 0

 4 11 2 0 0 0 0

 11 12 1 0 0 0 0

 12 13 2 0 0 0 0

 13 14 1 0 0 0 0

 14 15 2 0 0 0 0

 4 15 1 0 0 0 0

 3 16 2 0 0 0 0

 16 17 1 0 0 0 0

 17 18 2 0 0 0 0

 18 19 1 0 0 0 0

 19 20 2 0 0 0 0

 3 20 1 0 0 0 0

M END

$MOL

 ChemDraw 07189615442D

 7 7 0 0 0 0 0 0 0 0 1

 4.9383 -5.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 5.4383 -6.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 6.4383 -6.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 6.9383 -5.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 6.4383 -5.0883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 5.4383 -5.0883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 -6.9366 6.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1 2 1 0 0 0 0

 2 3 1 0 0 0 0

 3 4 1 0 0 0 0

 4 5 1 0 0 0 0

 5 6 1 0 0 0 0

 1 6 1 0 0 0 0

 4 7 2 0 0 0 0

M END

$MOL

 ChemDraw 07189615442D

 20 22 0 0 0 0 0 0 0 0 1

 -11.0316 7.4117 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0

 -11.0316 7.4117 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

 7.3000 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 9.0333 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 8.1667 -5.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 7.3000 -5.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 7.3000 -6.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 8.1667 -7.4117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 9.0317 -6.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 9.0317 -5.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 9.5333 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 10.5333 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 11.0333 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 10.5333 -4.0433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 9.5333 -4.0433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 6.8000 -4.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 5.7983 -4.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 5.2967 -4.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 5.7983 -5.7767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 6.8000 -5.7767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

 1 2 2 0 0 0 0

 1 3 1 0 0 0 0

 1 4 1 0 0 0 0

 1 5 1 0 0 0 0

 5 6 2 0 0 0 0

 6 7 1 0 0 0 0

 7 8 2 0 0 0 0

 8 9 1 0 0 0 0

 9 10 2 0 0 0 0

 5 10 1 0 0 0 0

 4 11 2 0 0 0 0

 11 12 1 0 0 0 0

 12 13 2 0 0 0 0

 13 14 1 0 0 0 0

 14 15 2 0 0 0 0

 4 15 1 0 0 0 0

 3 16 2 0 0 0 0

 16 17 1 0 0 0 0

 17 18 2 0 0 0 0

 18 19 1 0 0 0 0

 19 20 2 0 0 0 0

 3 20 1 0 0 0 0

M END

The MOLfile blocks, each starting with $MOL as a delimiter, give structural data for each molecule in the reaction and are written in the same order as the molecules in the reaction.


Standard Molecular Data File

The Standard Molecular Data file format (SMD file)is defined in the SMD File Format version 4.3 documentation, dated 04-Feb-1987. The following is a sample SMD file created using ChemDraw Pro for cyclohexanol (the line numbers are added for purposes of discussion only):

Line 1	>STRT cyclohexan
Line 2	>DTCR ChemDraw >CT	0 03-MAR-92 12:23:58
Line 4	15
Line 5	7 7 (A2,5I2) (2I4,4I2)
Line 6	C
Line 7	C
Line 8	C
Line 9	C
Line 10	C
Line 11	C
Line 12	O
Line 13	1 2 1
Line 14	2 3 1
Line 15	3 4 1
Line 16	4 5 1
Line 17	5 6 1
Line 18	1 6 1
Line 19	6 7 1
Line 20	>CO Points 8
Line 21	2 (2I8)
Line 22	24040	2700
Line 23	24040	900
Line 24	25600	0
Line 25	27160	900
Line 26	27160	2700
Line 27	25600	3600
Line 28	28715	3600
Line 29	>LB	2
Line 30	1 (I3,X,A)
Line 31	7:OH
A File in SMD Format for Cyclohexanol

Each line represents either a blank line, a block header line or a data record containing multiple fields of information about the structure. The SMD file is broken down into several blocks of information. The header for each block is preceded with a ">" sign. Individual fields are delimited by space(s) or a tab. The fields in the SMD format file used by ChemDraw Pro are discussed below. The field value for Carbon 6 from the example file is included in parentheses for reference.

1.	Line 1 starts the block named STRT. This block contains the molecule name. The molecule name is the file name when the file was created using ChemDraw Pro.

2.	Line 2 starts the block named DTCR. The information in this line includes the name of the application that created the file and the date and time when the file was generated.

3.	Line 3 starts the block named CT and indicates the number of records contained for the block; 15 in the above example. The information in this block includes the connection table(s) for the chemical structure.

4.	Line 5 contains four fields. The first field is the number of atoms, the second field is the number of bonds, the third field is the FORTRAN format for the number of atoms and the fourth field is the FORTRAN format for the number of bonds.

5.	Lines 6-12 each contains 1 field describing the atom type. The atom type can consist of only 1 element. Complete atom labels are not represented here, only the first atom of an atom label.

6.	Lines 13-19 of the CT Block each contains 3 fields describing the bonds between the atoms. The first field is the serial number of the atom from which the bond starts (1), the second field is the serial number of the bond ends (6). The third field indicates the bond order (1).

7.	Line 20 starts the block named CO, and indicates the units used in the picture (points, in this example) and the number of lines in this block, 8 in the above example. The information in this block includes the Cartesian coordinates of the atoms from the CT block. A right handed Cartesian system is used.

8.	Line 21 contains two fields. The first field is the scale factor required to convert the Cartesian coordinates into real coordinates. The second field is the FORTRAN format of the atom coordinates.

9.	Line 22-28 each contains the Cartesian coordinates for each atom indicated in the CT block.

10. Line 29 starts the Block LB, and indicates the number of records contained in the block, 2 in the above example.

11. Line 30 contains two fields. The first field is the number of atoms that have complete atom labels, the second field is the FORTRAN Format for the same.

12. Line 31 contains two fields that describes the complete atom label for any unresolved atoms in the structure. The first field is the serial number of the unresolved atom label (7) and the second field is the full atom label (OH).


Registering Your Software

To use CS ChemDraw you first must register the software using the registration code and serial number that comes with the product. The registration code and serial number are found on both the installation instructions sheet and the product box.

To enter your registration information:

·	Click in the name box and type your name.

·	Press Tab and type the name of your company.

·	Press Tab and type your serial number.

·	Press Tab and type your registration code exactly as it appears (case sensitive).

If you make a mistake in any of the boxes, you can press TAB to cycle through the boxes, press SHIFT+TAB to move to a previous box, or click within the box where you want to make a correction.

·	When all information is entered choose the Begin button.

The registration information is validated and the ChemDraw program is opened. The registration information you entered appears in the startup window each time you open ChemDraw for a new session. If you ever reinstall the software, you will need to enter this information again.

If you do not have the appropriate information and would like to register at a later time:

·	Choose theTry Again Later button.


About CS ChemDraw
About CS ChemDraw, Help Menu

Choose About CS ChemDraw to display a message box that displays information about the version and other information about the application you are using.


Actual Size, Tools

Choose Actual Size to return the document window to the original size after using the Show Page, Magnify or Reduce command.


Add Column, Tools Menu

Choose Add Column to add a column of Template panes to a Template panel.


Add Row, Tools Menu

Choose Add Row to add a row of Template panes to a Template panel.


Align submenu, Object Menu

Choose Align to display a submenu with several commands for aligning objects relative to one another. These commands are: Left edges, Left/Right centers, Right Edges, Top/Bottom edges centers, Top edges, and Bottom edges. When aligning structures or groups of structures you only need to select the bonds that you want aligned, after you choose an alignment, the entire structure moves to become aligned.


Analyze Structure, Structure Menu
Analyze Structure, Objects Menu

Choose Analyze Structure to calculate the formula, molecular weight, exact mass and elemental analysis of a selected structure, part of a structure, atom label or caption (in formula style). In addition, the valence, atom labels and nicknames within the structure or caption are checked for accuracy. You can paste the information as a caption by selecting a checkbox next to an analysis option and clicking the Paste button. The Analyze Structure command does account for isotopes. Isotopes are always assumed to be of natural abundance.


Apply Settings, File Menu

Choose Apply Settings to change the settings in the active document window to the settings in another document that you choose from the pop-up menu that appears. The pop-up listing contains all Style Sheets (except for Template Style Sheets): contained in the CD_ITEMS directory, and an Other command. If you choose the Other command, the Open dialog box appears in which you can select another ChemDraw document or Style Sheet not contained in the CD_ITEMS directory.


Arrow at End, Curves Menu

Choose Arrow at End to place an arrowhead at the end of the selected curve(s).


Arrow at Start, Curves Menu

Choose Arrow at Start to place an arrowhead at the beginning of the selected curve(s).


Atom Properties, Object Menu
Atom Properties, Structure menu

Choose Atom Properties to apply atom properties for creating query structures to atoms that are selected. Small characters appear on your structure when you apply atom properties. Click the Use Defaults button to remove atom properties from a selected atom(s).


Automatic, Text Menu

Choose Automatic to position atom labels automatically depending on the positions of the bonds to which they are attached.


Bold, Style submenu, Text Menu

Choose Bold to change selected caption or atom label text to a Bold style.


Bold, Curves Menu

Choose Bold to make selected curve(s) bold.


Bond Properties, Object Menu
Bond Properties, Structure menu

Choose Bond Properties to apply bond properties for creating query structures to bonds that are selected. Small characters appear on your structure when you apply bond properties. Click the Use Defaults button to remove bond properties from a selected bond(s).


Bring to Front, Object Menu

Choose Bring to Front to bring an object in the same picture layer all the way to the front of that picture layer.


Caption Text Settings, File Menu

Choose Caption Text Settings to display a dialog box with document settings that affect how new captions the active document are formatted. The layout of the dialog box is identical to the Format dialog box in the Text menu. Changing the Text Settings affects the active document only. All captions created after exiting the Text Settings dialog box will use the new settings. You can save caption text settings in Style Sheets if you repeatedly use the same settings.


Center on Page, Object Menu

Choose Center on Page to center an object(s) on the page. The centering is based on the center of the Selection rectangle.


Choose Center
Center, Text Menu

Choose to center all selected caption or atom label text. A check appears next to this command when it is selected.


Clear, Edit Menu

Choose Clear to remove selected objects from the active document window. Removed objects are not placed on the Clipboard.


Close, File Menu

Choose Close to close the active window. If you made changes since the last time you saved the document, you are asked to save the changes before the window is closed. Clicking the close box is equivalent to choosing Close from the File menu.


Check Structure, Object Menu
Check Structure, Structure menu

Choose Check Structure to check a selected structure for errors in valence, atom labels and nicknames.


Closed, Curves Menu

Chose Closed to add another curve segment that closes the selected curve segment.


Color Menu

The Color menu contains the foreground color and other available colors for coloring selected bonds, structures, atom labels, captions and non-bond objects. The foreground color is the color used for all objects unless you select an object and choose one of the other colors from the Color menu. Colors can be added by using the Color Palette command in the File menu.


Color Palette, File Menu

Choose Color Palette to display a dialog box where you can add, remove, or change the default foreground and background color and specify the other colors available for coloring objects. Changes made to the color palette affect the current document only. You can save Color Palette settings in a Style Sheet.

New Color: Click this button to access the Color Picker. Choose a color from the color wheel or set the color manually by entering values in the Saturation, Hue, Brightness, Red, Green and Blue control boxes. Click the OK button to add the new color to the Color palette.

Set Color: To change an existing color, select the color and click the Set Color button to access the Color Picker dialog box or double-click the color. Choose a color from the Color Picker and Click the OK button to change the selected color to the new color. All objects using the previous color are changed to the new color.

Remove Color: Select a color that you want to remove and choose the Remove button. Any objects using the removed color are changed to the Foreground color.


Contents, Help Menu

Choose Contents to display a list of help topics about CS ChemDraw from which you can choose.


Copy, Edit Menu

Choose Copy to place a copy of selected objects on the Clipboard. All items previously on the Clipboard are removed.


Copy As submenu, Edit Menu

Choose Copy As to display a submenu where you can choose to save a selected structure as a SMILES string or an SLN string on the clipboard for transferring to an application that can interpret the format.


Curves Menu

This menu contains commands for changing the style of selected curves. The choices are Plain, Dashed, Bold, Arrow at Start, Arrow at End, Half Arrow at Start, Half Arrow at End, Closed and Filled. You can apply one or more of the commands to a selected curve(s) , however, many of the commands are mutually exclusive. For instance, if Half Arrow at Start is selected, you cannot also choose Arrow at Start. A check appears next to each of the commands chosen for the selected curve(s). The selected styles are used for all new curves drawn, until you change the styles in the Curves menu.


Cut, Edit Menu

Choose Cut to remove the selected items from the document window and place them on the Clipboard. All items previously on the Clipboard are removed.


Dashed, Curves Menu

Choose Dashed to make selected curves(s) dashed.


Define Nickname Object Menu
Define Nickname Structure menu

Choose define nickname to display a dialog box where you can type a name for creating a nickname for the selected structure. This command is not available if there are no connection points or more than two connection points in the selected structure or a connection point to a double or triple bond. Defined nicknames can be used within an atom label to represent the expanded structure.


Delete Column, Tools Menu

Choose Delete Column to remove a column of Template panes from a Template panel. The column containing the selected Template pane is removed.


Delete Row, Tools Menu

Choose Delete Row to remove a row of Template panes from a Template panel. The row that contains the selected Template pane is removed.


Distribute Submenu, Object Menu

Choose Distribute to display a submenu with two commands for evenly spacing three or more objects horizontally or vertically relative to one another.


Drawing Settings, File Menu

Choose Drawing Settings to display a dialog box where you can specify the Document settings that affect how bonds are drawn. Changes made to drawing settings take affect for all bonds already drawn as well as those that are drawn later. Changes made affect the active document window only. Drawing settings can be saved in Style Sheets.

Chain Angle: The Chain Angle can be set anywhere from 1 to 179 degrees for drawing with the acyclic chain tool.

Bond Spacing: The spacing between double and triple bonds can be set as a percentage of the total length of the bond (between 1 and 100). This allows for proportional spacing to be used if different bond lengths are used in the drawing.

Fixed Lengths: The value entered in the box labeled "Fixed Length" constrains the length of the bonds drawn to this length when the Fixed Lengths command in the Tools menu is selected.

Bold Width: The value entered in the box labeled "Bold Width" determines the width of the line used when bold and wedge bonds are drawn.

Line Width: The value entered in the box labeled "Line Width" affects the width of all bonds, lines and arrowheads in the drawing.

Margin Width: The value in the box labeled "Margin Width" affects the amount of space surrounding all atom labels that will erase portions of the bonds to which they are attached. The margin width also determines the amount of white space surrounding the front bonds in a bond crossing.

Hash Spacing: The value in the box labeled "Hash Spacing" determines the spacing between the hashed lines used when wedged hashed bonds, hashed bonds, dashed bonds, dashed arrows or dashed curves are drawn.


Edit Menu

The Edit menu contains commands to undo actions you perform, to manipulate the contents of the active window and to convert structures in SMILES and SLN format.


Exit CS ChemDraw, File Menu

Choose Exit to close the ChemDraw application. You will be asked to save any changes that have been made to any open documents.


File Menu

The File menu contains commands used to manipulate ChemDraw documents, to print the contents of the active window, or to Exit the ChemDraw application.


Filled, Curves Menu

Choose this command to add a solid fill to the interior portion of the selected curve(s).


Fixed Angles, Tools Menu

Choose Fixed Angles to constrain the angles of any object to 15 degree increments relative to the X axis. If you hold down the ALT key while drawing you can temporarily turn off the Fixed Angles constraint (you will also turn off the Fixed Lengths constraint). Fixed Angles can be applied to all objects except Text and Reaction Mechanism Symbols.


Fixed Lengths, Tools Menu

Choose Fixed Lengths to draw bonds and orbitals with the Fixed Length set in the Drawings Settings dialog box. If you hold down the ALT key while drawing a bond you can temporarily turn off the Fixed Lengths constraint (you will also turn off the Fixed Angles constraint). DrawingChemicalStructures.4.


Flip Horizontal, Object Menu

Choose Flip Horizontal to flip selected objects from left to right.


Flip Vertical, Object Menu

Choose this command to flip selected objects from top to bottom


Flush Left, Text Menu

Choose Flush Left to align all the left edges of a selected caption or atom label. The right edges appear ragged. A check appears next to this command when it is selected.


Flush Right, Text Menu

Choose Flush Right to align all the right edges of a selected caption or atom label text so that they are flush. The left edges appear ragged. A check appears next to this command when it is selectedText.6.


Format, Text Menu

Choose Format to display a dialog box where you can change the font, size and style characteristics of a atom label or caption selectionText.6.


Font submenu, Text Menu

Choose Font to display a submenu listing the 10 last used fonts (in any document) from which you can choose to change the font of selected text (atom labels or captions). If the text that is selected is composed of multiple fonts, partial selection marks appear next to all fonts included in the selection to indicate that you will be changing many fonts to a single font

Other: Choose other to display a dialog box where you can select an alternate font to add to the Font submenu for the selected text.


Formula, Style submenu, Text Menu

Choose Formula to type chemical formulas. Choosing this command subscripts all numbers relative to other non numeric text.


Getting Started, Help Menu

Choose Getting Started to display a tutorial which you can use to learn the basic techniques for drawing a reaction scheme.


Group, Object Menu

Choose Group to combine several selected items into a single group. Grouped objects behave as an individual object when selected by double-clicking any part of the group using a selection tool. Individual objects within a group can be selected and manipulated as individual objects by clicking with a selection tool.


Half Arrow at End, Curves Menu

Choose Half Arrow at End to place a half-arrowhead at the end of the selected curve(s).


Half Arrow at Start, Curves Menu

Choose Half Arrow at Start to place a half-arrowhead at the beginning of the selected curve(s).


Chapter 16, Reference - Help Menu
Help Menu

The Help menu contains commands for accessing on-line help for CS ChemDraw.

About CS ChemDraw, Help Menu

Contents, Help Menu

Getting Started, Help Menu

Help Mode

How to Use Help, Help Menu

Search for Help on, Help Menu


How to Use Help, Help Menu

Choose How to Use Help to display a topics describing the use of the ChemDraw Help file.


Italic, Style submenu, Text Menu

Choose Italic to make the selected caption or atom label text appear in italic style.


Join, Object Menu

Choose Join to join selected bonds, atoms or curves into a single structure or curve. This command requires that the bonds, atoms or curve endpoints be with the tolerance value specified in the Preferences dialog box. The frontmost atom label or color appears in the resulting joined object.


Justified, Text Menu

Choose Justified to align the left and right edges of a selected caption so that they are flush. This command applies to captions only. A check appears next to this command when it is selected.


Label Text Settings, File Menu

Choose Label Text Settings to display a dialog box with document settings that affect how new atom labels for the active document are formatted. The layout of the dialog box is identical to the Format dialog box in the Text menu. Changing the Label Text Settings affects the active document only. All atom labels previously drawn will change to the new atom label settings. You can save label text settings in Style Sheets if you repeatedly use the same settings.


Line Spacing, Text Menu

Choosing Line Spacing to display a dialog box where you can specify the spacing between each line of the selected captions(s) or atom label(s).

Automatic: Click the Automatic radio button to make the spacing the height of the tallest character on any line in that caption or atom label.

Variable: Click the Variable radio button to make the spacing of each line the height of the tallest character on that line in the caption or atom label.

Fixed: Type a height in the box labeled "Fixed at" to make the spacing of the lines in the selected caption(s) a specific height measured in points.


List Nicknames File Menu

Choose List Nicknames to display a dialog box containing a list of the Nicknames available. In CS ChemDraw Pro, selecting a nickname and clicking the delete button removes the Nickname permanently.


Magnify, Tools Menu

Choose Magnify to increase the magnification of your view centered around a selected object. You can increase your magnification to a maximum of 400%, in four fixed increments.


New Document, File Menu

Choose New Document to create a new ChemDraw document. The name of the command changes to reflect the last Style Sheets used to create the new document


Object Menu

This menu contains commands that allow you to manipulate objects in the active document window.


Structure Menu

This menu contains commands that allow you to manipulate chemical structures in the active document window


Open, File Menu

Choose Open to open ChemDraw documents saved or documents saved in other file formats by choosing a file format from the List Files of Type drop-down list


Open Special submenu, File Menu

Choose Open Special to display a submenu listing Style Sheets and template documents that are stored in the CD_ITEMS directory. Choosing a Style Sheets opens an untitled document containing the Style Sheet settings and objects it contains. In CS ChemDraw Pro, choosing a Template document opens a Template window containing the Template document for editing.


Print Setup, File Menu

Choose Print Setup to display a dialog box in which you can specify the margins, orientation, paper size, and several print quality options for your ChemDraw document. The Print Setup dialog box options are dependent on the type and version of the printer you choose. Print Setup settings are document settings, and affect the current document only. Print Setup settings can be saved in a Style Sheet .

Page Size: Select the paper size that you will be printing on.

Margins: Type the left, right, top and bottom margins that you will be using for the paper size chosen. You cannot use margins that are smaller than those allowable for the printer driver you have chosen.

Orientation: Select a vertical(Portrait) or horizontal(Landscape) orientation for your document.


Paste, Edit Menu

Choose Paste to paste the current contents on the Clipboard into the active document window.


Plain, Style submenu, Text Menu

Choose Plain to remove all styles from the selected text


Plain, Curves Menu

Choose Plain to remove all styles from the selected curve(s).


Preferences, File Menu

Choose Preferences to display a dialog box where preferences that apply to the CS ChemDraw can be set.


Print, File Menu

Choose Print to display a dialog box where you can specify the number of copies of your ChemDraw document to print, among other options. The Print dialog box and the options it contains will differ depending on the printer you have selected. Printing.15.


Reduce, Tools Menu

Choose Reduce to reduce your magnification after you have used the Magnify command. You can also reduce your magnification below the actual size until the entire page fits on your screen.


Repeat, Edit Menu

Choose Repeat to repeat the last operation performed. The Repeat command is appended with the name of the last operation. For example Repeat Rotate, Repeat Move, and so on. Some commands are not repeatable and this command may read Repeat Not Available.


Revert, File Menu

Choose Revert to discard any changes that you have made to a document since the last time the document was saved or opened.


Rotate, Object Menu

Choose Rotate to display a dialog box where you have several options for rotating the selected object(s). You can enter a number in degrees to rotate the selection. If your selection includes structures that contain atom labels, you can choose to rotate the atom labels with the structure by selecting the Rotate Atom Labels check box. You can also double-click the Rotation handle on the selection rectangle to open the Rotate dialog box. In addition, you can hold down the CTRL key while dragging the Rotation handle on the Selection rectangle to rotate the atom labels with the structure


Save, File Menu

Choose Save to save the document in the active window. This command displays the Save As dialog box in which you can specify the name and location for saving the document. If you have previously saved the document in the active window, choosing this command will update the file with the most current version of the document. The Save dialog box will not appear in this case.


Save As, File Menu

Choose Save As to display the Save dialog box where you can specify the name and location of the file in which to save current file under a different name, in a different location or with one of the other file format available.


Save Style Sheet, File Menu

This command only appears when the active document window has no objects. Choose this command to save the current document settings within the Style Sheets used to create the document. WorkingWithDocuments.17.


Scale, Object Menu

Choose Scale to display a dialog box where you have several options for scaling the selected object(s). You can scale the selected objects so that the median bond length is equal to the length that is set in the Drawing settings dialog box. You can scale the objects so that the median bond is equal to a Fixed Length that you specify (the units are those set in the Preferences dialog box), or you can scale the selected objects by a percentage that you specify. If your selection includes structures that contain atom labels, you can choose to scale the atom labels with the structure by selecting the Scale Atom Labels check box. You can also open the Scale dialog box by double-clicking the resize handle on the Selection rectangle. In addition, you can hold down the CTRL key while dragging the Resize handle on the Selection rectangle to resize the atom labels with the structure.


Search for Help on, Help Menu

Choose Search to display a dialog box where you can specify and search for help information you want to view.


Select All, Edit Menu

Choose Select All to select the entire contents of the active document window or all the text in a text box.


Send to Back, Object Menu

Choose Send to Back to hide an object behind another within a layer. Objects will be sent all the way to the back of the layer.


Show Crosshair, Tools Menu

Choose Show Crosshair to display the Crosshair in the document window. You can use the Crosshair to position objects relative to one another. A check appears next to this command when it is selected. You can move the Crosshair to different parts of the document window by pointing to the intersection of the Crosshair axes, and dragging the pointer. You can constrain the movement of the Crosshair to the X axis or Y axis by holding down the ALT key as you drag. To remove the Crosshair, choose the Show Crosshair command again. The division marks on the Crosshair are based on the units you have set in the Preferences dialog box.


Show Page, Tools Menu

Choose Show Page to reduce the document window until it fits on the screen.


Show Rulers, Tools Menu

Choose Show Rulers to display rulers along the upper and left edges of the document window by choosing this command from the Tools menu. A check appears next to the Show Rulers command when the it is selected. To remove the rulers, choose the Show Rulers command again. The units of the ruler are those set in the Preferences dialog box.


Size submenu, Text Menu

Choose Size to display a submenu listing all of the available font sizes that you can choose from for changing the size of selected text (atom labels or captions). If the text that is selected is composed of multiple sizes, partial selection marks will be appear next to all sizes included in the selection to indicate that you will be changing many sizes to a single size.

Other: Choose other to display a dialog box where you can specify an alternate size to add to the Size menu for the selected text.


Stacked Above, Text Menu

Choose Stacked Above to make the first character in the last line of an atom label appear over a bond. If the atom label consists of a single line, this is equivalent to Flush Left justification. A check appears next to this command when it is selected.


Style submenu, Text Menu

Choose Style to display a submenu listing styles available that you can choose from for changing the style format of selected text. The Styles available are Plain, Bold, Italic, Underline, Subscript, Superscript and Formula. You can choose to apply one or more of the styles to the selected text, other than Plain. You can remove a single style by deselecting the command or remove all styles by selecting Plain Text.6.

Commands:

Bold, Style submenu, Text Menu

Formula, Style submenu, Text Menu

Italic, Style submenu, Text Menu

Plain, Style submenu, Text Menu

Subscript, Style submenu, Text Menu

Superscript, Style submenu, Text Menu

Underline, Style submenu, Text Menu


Subscript, Style submenu, Text Menu

Choose Subscript to lower the baseline of the selected text and reduce the font size by 25%.


Superscript, Style submenu, Text Menu

Choose Superscript to raise the baseline of the selected text and reduce the font size by 25%.


Text Menu

This menu contains commands used for formatting the text of caption(s) and atom label(s).

Commands:

Automatic, Text Menu

Center, Text Menu

Flush Left, Text Menu

Flush Right, Text Menu

Font submenu, Text Menu

Format, Text Menu

Justified, Text Menu

Line Spacing, Text Menu

Size submenu, Text Menu

Stacked Above, Text Menu

Style submenu, Text Menu


Tools Menu

This menu contains commands with which you can manipulate the contents of the active window.

Actual Size, Tools Menu

Add Column, Tools Menu

Add Row, Tools Menu

Delete Column, Tools Menu

Delete Row, Tools Menu

Fixed Angles, Tools Menu

Fixed Lengths, Tools Menu

Magnify, Tools Menu

Reduce, Tools Menu

Show Crosshair, Tools Menu

Show Page, Tools Menu

Show Rulers, Tools Menu


Underline, Style submenu, Text Menu

Choose Underline to underline the selected text.


Undo, Edit Menu

You can choose undo to undo an unlimited amount of actions. The only limitation to the number of actions you can undo is the amount of memory available to ChemDraw. Once you save a document, the Undo queue is deleted. A new queue is created from that point on.


Ungroup, Object Menu

Choose Ungroup to break up a grouped object into the original individual parts.


How to Use Help
How to Use ChemDraw Help

The help information in the topics below describe supplemental functions that are specific to the use of ChemDraw Help. You can learn the basic components of using the Help system by choosing the "Using Microsoft Help" topic or by choosing How to Use Help from the Help Menu in the ChemDraw Help menu bar.

Also See:

Displaying the Contents of ChemDraw Help

Accessing the ChemDraw Help Mode

Accessing Help for Menus and Commands

Accessing Help for Dialog Boxes

Searching for Topics


Displaying the Contents of ChemDraw Help

To open ChemDraw Help system and display its main contents:

·	Press F1

·	Or, choose Contents from the ChemDraw Help menu.


Accessing the ChemDraw Help Mode

The ChemDraw Help mode is context sensitive help which allows you to click a command, tool or screen element and display a help topic relevant to it.

To turn on the ChemDraw Help Mode:

·	Press SHIFT+F1

·	Or, choose Help Mode from the ChemDraw Help menu

The pointer changes to a lasso/question mark icon indicating that you are in help mode.

·	Clica tool, menu,command or screen element.

A help topic relevant to the item you clicked appears as the active window.


Accessing Help Menus and Commands
Accessing Help for Menus and Commands

To display a topic relevant to a menu:

·	Point to menu name and hold down the mouse button.

·	Press F1

To display a topic relevant to a command:

·	Open a menu and select (highlight) a menu command.

·	Press F1


Accessing Help for Dialog Boxes
Accessing Help from Dialog Boxes

To display a topic relavent to a dialog box while in that dialog box:

·	Open a dialog box

·	Press F1

·	Or, clicthe Help button within the dialog box.

A topic relevant to the use of the dialog box appears as the active window.


Searching for Topics

To open the ChemDraw Help system and search for a topic based on a keyword:

·	Choose Search for Help on.... from the Help menu

·	Type a keyword or select on from the list and click the Show Topics button

·	Select the topic of interest and click the Go To button

The topic you choose appears in the active Help window.

To perform another search when the help system is open.

·	Click the Search button in the ChemDraw Help window.


Help Mode Command

Choose Help Mode to use context sensitive help. Context sensitive help allows you to click a command, screen element or tool and automatically display a relevant topic in the ChemDraw Help system.

Also See:

How to Use ChemDraw Help


About ChemDraw
About CS ChemDraw

Contains version information about the copy of ChemDraw you are running.


Application Window

Contains the menu bar, tool window and document windows.


Control Menu Box

Contains commands useful for manipulating windows using the keyboard. Press

ALT+spacebar to open the Application Control menu followed by pressing the

underlined letter in the command that you want. Press ALT+hyphen to open the

document Control menu. In addition, double-clicking the Control menu box closes the

active window.

.


Drawing Area

The area of the document window where you can draw.


Maximize Button

Enlarges the document window to its maximum size by sharing the menu bar with the

application window. The maximize button of the application window enlarges the

application window to fill your screen. When you maximize a window, the Maximize

button changes to a Restore button (identified by having an up/down arrow as its

icon). The Restore button returns you to the last window size before you maximized.


Menu bar
Window Menu

Contains commands for arranging Open windows. At the bottom of the menu is a list of all the open windows. Choosing one of these windows brings it frontmost.

Cascade: Arranges open windows one in front of another with just enough of a window visible that it can be clicked and brought forward.

Tile Horizontal: Resizes all open windows so they can be displayed in a horizontal Row.

Tile Vertical: Resizes all open windows so they can be displayed in a vertical column.

Arrange Icons: Organizes all icons for minimized windows as a row at the bottom of the application window.


Window Menu
Menu Bar

Contains all the commands specific to the CS ChemDraw application for

manipulating documents and their contents.

Menu	Contents
File Menu	The File menu contains commands used to manipulate ChemDraw documents, to print the contents of the active window, or to Exit the ChemDraw application.
Edit Menu	The Edit menu contains commands to undo your last action, to manipulate the contents of the active window, to create publishers or subscribers, to convert structures to the SMILES format, and to display the Clipboard window.
Window Menu	Contains all open ChemDraw Documents. In CS ChemDraw Pro the Window menu also contains open Template documents. Choosing a document from the Window menu makes it the active window.
Object Menu	The Object menu contains commands with which you can manipulate a selected object.
Color Menu	The Color menu contains the foreground color and other available colors for coloring selected bonds, structures, atom labels, captions and non-bond objects. The foreground color is the color used for all objects unless you select an object and choose one of the other colors from the Color menu. Colors can be added by using the Color Palette command in the File menu. .
Text Menu	The Text menu contains commands for formatting and justifying caption and atom label text.
Tools Menu	The Tools menu contains commands that help you create drawings
Curves Menu	The Curves menu contains commands for applying styles to selected curves
Help Menu	Contains commands for accessing on-line help for CS ChemDraw.


Minimize Button

Converts the active document or application window (and all its document windows)

to an icon. Double-clicking the minimized icon restores the window.


Scroll Arrow

Scrolls the document window in small increments in the direction of the arrow.


Scroll Bar

Scrolls the document window in large increments.


Scroll Box

Scrolls the document window in the direction as you can drag the box.


Title Bar

Contains the name of the application or document as a Window Title. Also, the Title

bar can be dragged to move a window.


Tools Window

Contains icons representing the drawing tools available in CS ChemDraw. Click a

tool icon to select it. The selected tool determines what drawing operation is carried

out if you click in the document window. You can move the Tools window by dragging

its Title bar.


Window Border

Enlarges or shrinks a window in one direction when dragged.


Window Corner

Enlarges or shrinks a window in either directions when dragged.


Document Window

The window in which you draw.


Show Toolbar

Choose this command to toggle the display of the ChemDraw toolbar.


Structure menu

Contains commands for manipulating selections containing chemical structures.