How to use this guide

The Felix 2002 User Guide is a basic guide to working with the FELIX software.

There are two ways to access the online version of this book:

Any updates or corrections will be posted to the web site, making the information at the most current.

Note: : If you are prompted for a username and password at the Accelrys documentation website, use the following:

Username: science

Password: faster

An index and table of contents are provided You can also use the Accelrys Site Search at:" target="_blank">

Select All Documentation in the Search Area list. Enter term(s) in the Search field, then click Search.

While viewing the document online, you can use the searching capabilities of your browser to locate information.

You can print individual chapters of these documents via your browser's printing capability.

For information about the FELIX command language or to access the tutorials, please see the online FCL Command Language Reference and FELIX Tutorials books.

Using this book

The general information contained in the main body of this manual include the information described in "Topics covered" below.

The FELIX User Guide also contains several appendices. These provide additional information that might make installing and running FELIX easier.

Who should use this book

This book is intended as a basic guide to FELIX for both novice and advanced users of the program. Novice users will also want to look at the FELIX Tutorials, while advanced users may want to also consult the FELIX Command Language Reference.

The FELIX User Guide discusses the basic use of FELIX, including:

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

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

What does FELIX do?

FELIX is an interactive program for processing, displaying, and analyzing data acquired on nuclear magnetic resonance (NMR) spectrometers.

A complete NMR data processing and analysis program, FELIX provides you with tools for efficiently transforming NMR data of almost any dimensionality and for processing, displaying, storing, and retrieving the resulting spectral information.

FELIX is flexible and efficient to use. It can run either as a menu-driven graphical interface or as a concise and powerful command-driven program (via the FELIX Command Language: FCL). In addition, the FELIX macro processor enables you to automate lengthy and complex processing procedures (for example, routine or ND data processing). FCL is powerful enough to permit you to create your own menus and user interface or to customize the existing menus.

The quantity and variety of data that FELIX handles, ranging from peak integrals to assignment names of ND peaks, demands powerful data storage and management features, which are provided by the FELIX database. The database is accessible from many FELIX functions (e.g., the peak pickers and assignment interface), from the command line, or from within macros. The tools provided by the database allow you to quickly store data temporarily or permanently in files, to display the data as lists, and to edit the spectral information using a table interface. The database also sorts data into lists according to user-defined criteria and can compare lists for similarities or differences.

Feature list

FELIX's major functions include general features for NMR spectral processing and basic analysis, and specialized module features for biomacromolecular resonance assignment and receptor-ligand binding analysis. You may need to obtain ND, Assign, or Autoscreen license privileges to access the special features of FELIX.

General features

Special features for ND processing

The ND license allows you to access the following capabilities in addition to the general features in FELIX 2004.

Assign module features

2D TOCSY, COSY, and/or NOESY spectra

3D homonuclear spectrum (e.g., 3D TOCSY-NOESY)

3D 15N HSQC (or HMQC)-TOCSY spectrum

2D 15N-1H HSQC and 3D 15N HSQC-TOCSY spectra

3D HNCO, HNCA, and HN(CO)CA spectra

3D CBCANH and CBCA(CO)NH spectra

2D 15N-1H HSQC and 3D CBCANH and CBCA(CO)NH spectra

3D HNCO, CBCANH, and CBCACO(N)H spectra

3D HNHA, CBCANH, and CBCA(CO)NH spectra

4D HNCAHA and HACA(CO)NH spectra

3D HCCH-TOCSY spectrum

3D H(CC-TOCSY)(CO)NH spectrum

2D NOESY spectrum

3D homonuclear NOESY spectrum (e.g., 3D NOE-NOE)

Autoscreen module features

Starting FELIX

Before reading this section you must have successfully installed FELIX.

You can start FELIX either by double clicking the FELIX 2004 icon on your desktop, or by clicking the Start button on the task bar, then selecting Programs/Accelrys FELIX 2004/FELIX 2004.

When FELIX is started, it reads a felixrc.ini file in the installation directory. This file defines the paths that FELIX searches to find macros, menus, data, and other files. If necessary you can edit this file to customize it.

The FELIX product includes the macros and menus that are required for the FELIX program to start and run. These macros, menus, schema, and any other files that are essential for running FELIX are placed in runtime directories, as shown in the following figure..

Note: ACCELRYS_FELIX2004 is the environment variable created while FELIX is installed on your computer. It points to the folder where the FELIX executable files are located. By default the installation folder is C:\Program Files\Accelrys\FELIX 2004.

For further details on starting FELIX and for tutorials on using it, please see FELIX Tutorials.

Related books

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

Typographical conventions

Unless otherwise noted in the text, this book uses these typographical conventions:

Select the Assign pulldown.