Chem3D ViewerȘ
© 1991-1992, Cambridge Scientific Computing, Inc.  All rights reserved worldwide.

6 things you can quickly do with a Chem3D model using Chem3D Viewer:

„ Choose the Replay command from the View menu to see a Chem3D movie. Click the Stop button to stop the movie.

„ Select the Trackball tool (the second icon in the Tools window) and perform real-time rotation of the entire molecule.

„ Select the Select tool (the first icon in the Tools window) and move the pointer over atoms and bonds to display information about them. You can also display other information by clicking atoms and bonds to select them.

„ Hold down the mouse button while pointing to one of the four rotation bars (located around the periphery of the window containing a model) and drag along the rotation bar.  You can perform real-time rotations about the X Axis, about the Y Axis, about any axis defined by two atoms, or around a bond.

„ Choose the commands in the Analysis menu to display bond lengths, bond angles, dihedral angles and close contacts.

„ Using System 7, choose Show Balloons from the Help menu to display help balloons describing every item on the desktop and every menu command.

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Welcome to Chem3D Viewer. Chem3D Viewer is an application used to examine molecular models created using Chem3D and Chem3D Plus. This document briefly describes some of the features available in Chem3D Viewer.

All of the features of Chem3D Viewer are available in CSC Chem3D (except for color display options) and CSC Chem3D Plus (which includes color display). You can learn many of the ways that models can be manipulated in CSC Chem3D by working with models in Chem3D Viewer. However, Chem3D Viewer is a viewing tool only;  you cannot save your work from Chem3D Viewer and you cannot create models.  

CSC Chem3D and CSC Chem3D Plus contain many other features that you can use to manipulate and analyze models. A summary of these features is included at the end of this document.

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Table of Contents

Rotating Models
Working with Atoms and Bonds
Changing the Appearance of a Model
Table Windows
The Menus in Chem3D Viewer
Things You Can Do in Chem3D That You Cannot Do in Chem3D Viewer
Things You Can Do in Chem3D Plus That You Cannot Do in Chem3D or Chem3D Viewer
For More Information

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Rotating Models

Four rotation bars are located on the periphery of each Model window. You can use these rotation bars to rotate the model around different axes.  

To perform a rotation about the X axis:

„ Hold down the mouse button while pointing to the X-axis rotation bar, located along the right side of the Model window.  
„ Drag the pointer along the rotation bar and release the mouse button.
  
To perform a rotation about the Y axis:

„ Hold down the mouse button while pointing to the Y-axis rotation bar, located along the bottom of the Model window.  
„ Drag the pointer along the rotation bar and release the mouse button.
  
To rotate around an axis defined by two atoms:

„ Select exactly two atoms.  
„ Hold down the mouse button while pointing to the rotation bar above the model.  
„ Drag the pointer along the rotation bar and release the mouse button.
  
To rotate part of a molecule around a bond:

„ Select a bond between two parts of a molecule.
„ Hold down the mouse button while pointing to the rotation bar at the left side of the Model window.  
„ Drag the pointer along the rotation bar and release the mouse button.

Instead of specifying the bond around which you want to rotate, you can select a group of atoms and those atoms will rotate around the bond connecting them to an unselected atom.

Finally, you can freely rotate the model using the Trackball tool, the second tool in the Tools window. To freely rotate the model:

„ Select the Trackball tool from the Tools window. 
„ Move the pointer inside of the circle that appears in the center of the Model window and hold down the mouse button.  

As you drag the pointer, the model will follow the movement of the pointer. If you move the pointer outside the trackball circle, the model rotates around the Z axis.

With CSC Chem3D, you can create several pictures of your model and store these pictures in a series of views. To display different views of your model, use the view scroll bar, located along the right side of the Model window. When you click the arrows at the top or bottom of the scroll bar, the view one back or forward appears. When you click the gray regions above or below the scroll box, the view ten back or ten forward appears. To display a particular view, drag the scroll box of the view scroll bar.

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Working with Atoms and Bonds

Before performing certain operations on an atom or bond, you must select it to distinguish it from other atoms and bonds. Atoms and bonds are selected using the Select tool, the first Tool in the Tools window. 

To display information about an atom or bond:

„ Position the pointer over the desired atom or bond.
A box appears, containing relevant information about the atom or bond.

To select an atom or bond:

„ Click the atom or bond while its information is visible.

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Changing the Appearance of a Model

You can change a variety of settings which affect the way your model appears using the Preferences window. To display the Preferences window:

„ Choose Preferences from the Windows menu.

Along the left side of the Preferences window is a group of buttons. Each button corresponds to a control panel. To display a control panel:

„ Click its button.

The preferences in the Model Display control panel determine what shapes, patterns and colors are used to represent the atoms and bonds in your model. Note: some of the preferences in the Model Display control panel are only available on computers that supports color. If you are using a computer that does not support color, these preferences will not appear.

The Atom and Bond Sizes control panel contains preferences which you can use to determine the sizes of the atoms and bonds in your model.

Use the Atom Labels control panel to modify the way in which atom labels appear. Atom labels consist of a symbol and a serial number.

The Stereo Views control panel contains a checkbox that you can select to view and manipulate two different views of your model at the same time.

The Pointing Information control panel contains checkboxes that you can select to determine what information appears about atoms and bonds as you pass the pointer over them.

The Clicking Information control panel contains checkboxes that you can select to determine what information appears as you click atoms or bonds.

The Movies control panel contains preferences which affect the creation of different views and how you want the views of your model to replay as a movie.

The Scaling control panel contains a checkbox that you can click to specify whether you want the model to be automatically resized after performing operations such as moving a bond to an axis (using commands in the View menu) or resizing the Model window. In CSC Chem3D and CSC Chem3D Plus, this control panel is called the Building control panel. It contains other preferences that you can use to specify how CSC Chem3D performs building operations used to create molecules.

The Text control panel contains a font selection menu and font size control for choosing the font and font size used to display text in Table windows (see the next section). This font is also used for information that appears in the status bar (located at the top of a Model window) and for information that appears as you point to atoms and bonds.

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Table Windows

Other windows in Chem3D Viewer display information about models. The information available in these windows appears in tables, similar to spreadsheets.  

The Measurements window contains internal measurements between various atoms in your model. Measurements are organized primarily by type; all of the bond lengths are listed first, then the interatomic distances, then the bond angles, and then the dihedral angles.  Within measurements of the same type, the measurements are organized by serial number.

The Measurements window appears whenever you specify a measurement to be shown, by either choosing one of the Set Measurement commands (Set Bond Length, Set Distance, Set Bond Angle or Set Dihedral Angle) from the Build menu, or one of the commands at the bottom of the Analysis menu (Bond Lengths, Bond Angles, Dihedral Angles, or Close Contacts).

The Messages window contains messages generated by Chem3D Viewer regarding your model. You can make the Messages window appear by choosing Deviation from Plane from the Analysis menu.

The Cartesian Coordinates window contains the atom name and the X, Y and Z coordinates for each atom in a model.

CSC Chem3D and CSC Chem3D Plus contain additional table windows that display other information about models.  Also, you can manipulate the parameters used to build models using Table windows.  In CSC Chem3D, you can also modify the positions of atoms in a model by editing the contents of the Measurements window or the Cartesian Coordinates window.

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The Menus in Chem3D Viewer

All of the menus and menu commands in Chem3D Viewer are also found in CSC Chem3D and CSC Chem3D Plus. This section gives a brief summary of each menu. If you choose a dimmed command, a window appears explaining why the command is not available.

To retrieve model documents, use the File menu.

The Edit menu contains the standard Macintosh editing commands. At the bottom of the Edit menu are commands used to select groups of atoms.

To temporarily hide groups of atoms, use the commands in the Hide menu.

To display the selected measurement in the Measurements window, choose one of the Set Measurement commands (Set Bond Length, Set Distance, Set Bond Angle or Set Dihedral Angle) from the Build menu. The rest of the commands in the Build menu are used to either display the atom labels for the selected atoms, and to set the color of the selected atoms.

To orient selected atoms to the axes and planes of the Cartesian coordinate system, to create Chem3D movies and to scale models to different sizes, use the commands in the View menu.

While you are playing movies of a model, a window appears that contains a Stop button. To stop a movie, click the stop button or press the Escape key or hold down the Command key while typing a period.

To analyze the three-dimensional shape of your model and to display various measurements associated with your model, use the commands in the Analysis menu.

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Things You Can Do in Chem3D That You Cannot Do in Chem3D Viewer

Open files created using CSC ChemDraw and convert two-dimensional structures into three-dimensional models.

Open files in a variety of file formats such as Cambridge Crystal Data Bank, Protein Data Bank, MOPAC, SYBYL MOL, SYBYL Mol2, and others.

Save models either in Chem3D's file format, PICT, PICS, or Encapsulated PostScript.  You can also save models in the above file formats.

Print models and table windows.

Transfer pictures of molecules into other applications using the commands in the Edit menu.

Manipulate the set of parameters used to build models.

Build models using drawing tools and a collection of pre-existing fragments (ring systems, amino acids, functional groups, etc).

Build models by specifying text (such as "CH2CH3" or "AlaProMetOH") that CSC Chem3D can automatically expand into a group of atoms and bonds.

Store substructures that you can use to build larger molecules.

Structural error minimization.

Dock separate molecules.

Overlay separate molecules.

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Things You Can Do in Chem3D Plus That You Cannot Do in Chem3D or Chem3D Viewer

Open files in even more file formats such as MDL MolFile, Molecular Simulations MolFile, MacroModel and others.

Energy Minimization.

Molecular Dynamics.

Steric Energy computations.

Single Point Light Source Shading.

Print Models in Color.

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For more information please contact us at:

Cambridge Scientific Computing, Inc.
875 Massachusetts Avenue
Cambridge, Massachusetts 02139 U.S.A.
Tel: 617 491-6862    Fax: 617 491-8208
Internet: info@camsci.com
AppleLink: CSC.COM