How to use this guide

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

There are two ways to access the online version of this book, at Accelrys's website (http://www.accelrys.com/doc/) or from the installed FELIX files. Any updates or corrections will be posted to the website, making the information at www.accelrys.com the most current.

An index and table of contents are provided, and you are encouraged to make use of the searching capabilities of your browser to locate information if you are reading this online.

Please see the online help for more information about the controls in the menu interface. 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

In addition to the general information contained in the main body of this manual, the FELIX manual also contains several appendices. Before running the program, we suggest you browse through these for additional information that might make installing and running the program easier.

Appendix A, References, contains complete references for citations made in the text of this manual.

Appendix B, Keyboard Shortcuts and Accelerator Keys, lists keyboard shortcuts for the commands in the interface.

Appendix C, FELIX Startup gives helpful hints on starting FELIX the first time.

Appendix D, Data Transfer and Conversion gives information on converting various data formats into FELIX-compatible input.

Appendix E, Data Files list important file formats.


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 book 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 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

Following is a survey of the major functions provided by FELIX.

General features

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

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)

3D 15N HSQC (or HMQC)-NOESY spectrum.

Triple resonance spin systems.

Model module features

Autoscreen module features


Starting FELIX

Before reading this section you must have successfully installed FELIX.

There are two methods for starting FELIX. One method is to start FELIX as a standalone program by entering felix at the system prompt. You may also start FELIX from within Insight II by clicking the Accelrys logo and selecting NMR_Refine from the resulting list. Once you are within the NMR_Refine module, select the FELIX/Start_FELIX menu item. After verifying that the correct executable file is listed in the resulting control panel, select Execute.

When you start the latest FELIX software for the first time, a FELIXRC INFORMATION dialog box informs you that it will create a .felixrc99 file in your home directory. This file defines the paths that FELIX searches to find macros, menus, data, and other files. You can choose between two different directory tree structures. The first choice, Use only current directory, means that all files you create will be placed in your current working directory. The second choice, Use multi-directory system, creates a set of user directories within your current working directory, in which all user-created files will be stored (this is similar to the directory tree structure for FELIX 230, where it was called "user defined directories"). The multi-directory system structure is shown in the following figure.

Once the .felixrc99 file is created, you can edit this file to customize it. If you had customized the .felixrc97 file for previous versions of FELIX, you have to copy those changes to .felixrc99 for them to take effect.

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:

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

If you experience difficulties in running FELIX, please refer to the troubleshooting section in the Insight System Guide.


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 Model pulldown.