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:

at Accelrys's website:

http://www.accelrys.com/doc/life/index.html

FELIX installation CD

Any updates or corrections will be posted to the web site, making the information at www.accelrys.com 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:

http://www.accelrys.com/search.html" target="_blank"> http://www.accelrys.com/search.html

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.

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

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 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 User Guide discusses the basic use of FELIX, including:

Working with the interface

1D, 2D, and ND processing of NMR data

Visualization of data

Theory of NMR processing

Hot-key reference

File formats

FELIX startup

Data transfer and conversion

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

The windowing software on your workstation

Use of the mouse on your workstation

Basic DOS commands

The FELIX menu interface

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

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

Platform-independent data file transfer between machines without file conversion.

Direct reading of native spectrometer FID files from different vendors (Bruker, Varian, JEOL).

Zero-filling of data sets.

Linear prediction of the first and last points of an FID, with or without root reflection.

Linear prediction of last points using mirror image methodology.

DC offset correction.

Window functions: exponential, sinebell, sinebell squared, skewed sinebell, skewed sinebell squared, Gaussian, trapezoidal, Kaiser, and convolution difference.

Fourier transforms: complex fast Fourier transform (FFT), Bruker FFT, inverse FFT, real FFT and digitally oversampled FFT for Bruker data.

Generation of complex data from real data for phasing using Hilbert transform.

Baseline correction with automatic and manual baseline point selection; also cubic spline and polynomial baseline correction.

Solvent suppression using time domain convolution, LP-SVD, and polynomial fitting.

Spectrum phasing: automatic, real-time, and manual.

Data buffer stack for easy storage and retrieval of free induction decays (FID's), spectra, and other plots, allowing comparison

and point-by-point arithmetic operations between pairs of data buffers.

Integration of the full spectrum of segments and integral values displayed on plot (and stored in database).

Automated 1D line fitting for obtaining accurate integrals of noisy or poorly resolved data.

Automatic or manual peak picking of 1D and 2D data; labeling of picked peaks with axis units.

Enhanced peak picking using example peaks.

2D peak fitting and peak modeling.

J-coupling extraction for 2D DQF and E-COSY spectra.

J-coupling extraction based on heteronuclear E-COSY, FIDS, FIDS-E-COSY, and DQ-ZQ methods.

Easy page setup, print preview and printing.

Display features that include spectrum expansion, real plots, imaginary plots, and real/imaginary plots for 1D data or 1D slices of 2D data.

Menu access for rapid, customized 1-D processing.

Matrix storage of two-dimensional (2D) data for easy access to t1 and t2 data vectors.

Supplied macros for simplified processing of states, TPPI, states- TPPI, and N/P 2D data.

Enhanced contour plot for accurate and fast representation of peak intensity in two dimensions.

Intensity plot for fast 2D data display of positive and negative peaks.

Volume integration in two dimensions.

Database tools for storing and correlating peak assignments.

Tile plot to display isolated sets of overlapping peaks, simplifying identification of related peaks.

Correlated cursors to permit accurate comparison of peak positions in several graphics frames at one time.

Flexible frame connection to analyze multiple nD spectra concurrently.

Keypad navigation within plots.

Lists that allow you to sort and compare information (e.g., cross peak data from the database).

Matrix compression to reduce 2D data set storage requirements, with minimal loss of spectral information.

Importing processed data from other processing/analysis software: NMRCompass, NMRPipe, Bruker, and Varian.

Flexible restraint generation tools for NOE-distance, NOE-volumes, 3J-dihedral, and ambiguous NOE-distance and NOE-volume categories--either in Discover/DG-II or X-PLOR format.

Relaxation-time analysis for 2D heteronuclear data.

Table interface to the database.

Platform-independent data file transfer between machines without file conversion.

Direct reading of native spectrometer FID files from different vendors (Bruker, Varian, JEOL).

Special features for ND processing

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

3D transformation macros for states, TPPI, states-TPPI and N/P data.

Plane transformation for 3D states, TPPI, states-TPPI and N/P data.

4D transformation macros for states, TPPI, states-TPPI and N/P data.

Distributed processing for 3D and 4D transformation.

Rapid "bundle mode" access to matrix vectors.

Convenient display and analysis of 2D planes in 3D and 4D matrices from any direction.

Keypad navigation between planes.

Slider control for plane selection.

Convenient access to 1D vectors from 3D and 4D matrices.

3D/4D peak picking and volume integration.

Enhanced peak picking using example peaks.

3D/4D cross peak filtering.

3D/4D cross peak modeling.

Matrix compression to reduce 3D/4D data set storage requirements, with minimal loss of spectral information.

Assign module features

Comprehensive features to organize the assignment project in a database.

Define up to 12 spectra in one experiment.

Overlay multiple contour plots in real time.

Overlay multiple peak entries on contour plots.

Tile and strip plots from frequency clipboard, spin systems (patterns), or prototype patterns.

Display frequency clipboard or frequencies of spin systems (patterns) or prototype patterns on plots.

Automated routines for detecting spin systems via systematic search in:

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

Automated routine for detecting spin systems via simulated annealing in 2D TOCSY, and 2D COSY and/or 2D 13C-1H HSQC spectra.

User-tailorable semi-automated routine to exploit virtually any combination of heteronuclear double and triple resonance experiment to detect spin systems.

Fuzzy algebra-based procedures for verifying new patterns.

Library-based identification of patterns and frequencies using all-atom matching or the C -C combined chemical shift expectation value method.

Sequential connectivity detection routine based on:

2D NOESY spectrum

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

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

Triple resonance spin systems.

Rule-based approach to make sequence-specific assignments.

Simulated annealing-based approach to make sequence-specific assignments.

Tools to visually inspect and manually override the results of automated methods in all stages of the assignment procedure.

Point-and-click manual assignment of frequencies or peaks.

Automated peak assignment of up to 4D spectra based on assigned patterns for NOE and/or COSY type spectra; generating and storing ambiguous (multiple possible) assignments.

Chemical shift index calculation based on H , C , and C chemical shift libraries.

Tool for generating reports about the assignment of patterns.

Autoscreen module features

Comprehensive features to organize a 1D or 2D SAR by NMR-like project in a database.

Unlimited number of 2D 15N-HSQC spectra can be processed, plotted, and reviewed.

Unlimited number of 1D spectra can be processed, plotted, and reviewed.

Automated processing of spectra based on parameters from a control spectrum.

Novel algorithm for automated phasing of ND spectra.

New algorithm for automated baseline correction.

Innovative scoring algorithms that provide reliable peak-matching and -identification in situations where peaks in a reference spectrum disappear or additional peaks appear in spectra of protein-ligand complexes.

Use of peak shape, including both peak widths and heights, for reliable peak matching and scoring.

New progressive peak tracing (PROPET) algorithm that provides more reliable peak matching by taking advantage of titration spectra.

Automated peak matching and scoring of an unlimited number of test spectra.

Tools for overlaying multiple contour plots in real time and displaying peak displacements.

Tools for defining and using a selected subset of peaks (region of interest) for scoring.

Tools for generating reports about interesting spectra (high-affinity ligands) and interesting peaks (binding subsites) and for Kd fitting.

Connection to Insight II to display molecular structure of ligand and protein.

Automated coloring of peak displacements on protein surface displayed in Insight II.

Exporting scores to Cerius2 study tables for further analysis using QSAR tools.

Clustering experiments and peaks for identifying individual binding subsites in a protein.

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:

FCL Command Language Reference - provides information for advanced FELIX users about using FCL and the command mode of FELIX.

FELIX Tutorials - Contains step-by-step examples to help you learn to use FELIX.

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

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

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 book uses these typographical conventions:

Names of pulldowns, menu items, command names, and other things in the FELIX interface are presented in bold type. For example:

Select the Assign pulldown.

FELIX output and file samples are presented in a courier font. If the example indicates something you must type, it is given in bold courier font. For example:

     > mat yuin.mat

In referring to the menu items that are used when running FELIX through its menu interface, this guide uses the format Pulldown/Command, since you use the mouse to select the pulldown first, before the command name appears. Where there is more than one cascading pulldown to access before the command name appears, the pulldowns are simply given in the order that you select them.