Cerius2 Modeling Environment

1       How To Use This Guide

Important

This documentation set, Cerius² Modeling Environment, is a complete guide to the Cerius² modeling environment. It describes the integrated set of tools for session management and atomistic modeling that form the core of the Cerius² modeling environment. Topics described include molecular modeling tasks and their associated Cerius² procedures, combining conceptual, procedural, and reference material in one comprehensive information source.

Using this guide

You need not read this entire documentation set before you start using Cerius²:

• First-time users should read Introducing Cerius2 first.

• Everyone should read How To Use This Guide, which introduces the Cerius² modeling environment, and at least skim these sections, which describe how to perform basic modeling tasks:

The Cerius2 Interface

Building Models

Managing Models and Sessions

Geometry Analysis

Viewing and Displaying Models

• You can glance through the headings in these sections, which describe modeling and other tasks that typically are performed less often or by fewer users:

Enhancing Model Display

Working with Graphs

Working with Tables

Scripts and Licensing

Customizing the Interface

You can then read those sections that describe the tasks you want to perform and/or tools you want to use.

• Reference material is contained in these sections:

References

Definitions

Mouse and Keyboard Actions

File Formats

Prerequisites

You should already be familiar with:

• The windowing software on your workstation.

• Use of the mouse on your workstation.

• Basic UNIX commands.

• A licensed copy of Cerius² installed.

• A home directory in which you have write permission.

On-screen help is available within the Cerius² environment. It is accessed by clicking the right mouse button while the cursor is over the item in the interface about which you want information. A brief identification of some items appears when you simply allow the cursor to linger over them. Additional help and some demos are accessed from the Help menu.

Other Cerius2 documentation

• Cerius² Builders--Discusses the specialized builder modules that can be added to supplement the basic model sketching capabilities provided by the Cerius² modeling environment (that is, the Analog Builder, Crystal Builder, Surface Builder, Interface Builder, Polymer Builder, and Amorphous Builder modules).

• Cerius² Tutorials--Several guides illustrating the use of Cerius².

• Forcefield-Based Simulations, CDiscover, and Cerius² Simulation Tools--Discuss forcefields and orcefield-based calculations; CDiscover in the Cerius² and standalone modes; and the Open Force Field, Force Field Editor, Charges, Minimizer, Dynamics Simulation, and Analysis modules.

• Command Script Guide--Shows how to capture and replay a script of Cerius² commands and how to enhance your command scripts with the features of the Tool Command Language (Tcl).

• Cerius² Installation and Administration Guide--Provides step-by-step instructions for installing and administering Cerius² in your operating environment.

• Terms introduced for the first time are presented in italic type. For example:

Instructions are given to the software via control panels.

• Keywords in the interface are presented in bold type. In addition, slashes (/) are used to separate a menu item from a submenu item. For example:

Select the View/Colors... menu item means to click the View menu item, drag the cursor down the pulldown menu that appears, and release the mouse button over the Colors... item.

• Words you type or enter are presented in bold type. For example:

Enter 0.001 in the Tolerance entry box.

• UNIX command dialog and file samples are represented in a typewriter font. For example, the following illustrates a line in a .grf file:

	CERIUS Grapher File

• Words in italics represent variables. For example:

>	cerius2 -b outputfile scriptfile

In this example, the actual name of the file to which text output should be directed replaces the value outputfile, and scriptfile is replaced with the name of a file containing the desired command script.