How to use this book

The online FCL Command Language Reference is a complete guide to the command language that underlies the FELIX program. Contained within its pages is information about the basics of the language, symbols and expressions, macros, real-time displays, menus (and how to customize them), the database, and commands. Appendix C contains some useful example macros.

This reference is available only online. An index and table of contents are provided, and you may use the searching capabilities of your browser to locate information.

If you want, you may print individual chapters of this guide using your browser's printing capability.

Note: Appendices A and B are very large files. You may want to be certain you need all the information these sections contain before printing them.

Please see the online help for more information about the commands in the menu interface. For information about using FELIX, please consult the FELIX User Guide and FELIX Tutorials books.

Who should use this guide

This guide is primarily intended for advanced FELIX users who are interested in modifying the user interface, writing macros, and doing other operations that require the FELIX command language FCL.

What FCL does

Some of the things FCL allows you to do are:

Modify the menu interface.

Write your own macros.

Modify existing macros.

Things to be familiar with

You will probably want to familiarize yourself with a few things before working with FCL:

The windowing software on your workstation.

Use of the mouse on your workstation.

Basic UNIX commands.

The FELIX menu interface.

Workstation requirements

Before you begin, be certain that you have these things available on your workstation:

An installed and licensed copy of FELIX.

A directory in which you can create subdirectories and files.

Related books

You can find additional information about general molecular modeling, structure determination, and NMR data analysis in several other books published by MSI:

NMRchitect -- Describes the theory of NMR data analysis and describes how to use the NMRchitect software to analyze NMR data in the Insight II envirnment.

Insight II -- Describes the Insight II molecular modeling program.

System Guide -- Provides step-by-step instructions for installing and administering Insight II products in your operating environment.

Typographical conventions

Unless otherwise noted in the text, this guide uses the typographical conventions described below:

Names of most items in the Insight II or Cerius² interface are presented in bold type. For example:

Select the Transform/Rotate menu item.

UNIX command lines are represented in a courier font. If the line contains keywords you must type exactly, they are given in bold courier font. If a word is something you must replace with a specific value (like a filename), it is indicated in italic bold courier font. For example:

     > cerius2 -b output scriptfile