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:

Working with the interface.

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

Visualization of data.

Assignment.

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 UNIX^{^Ž} 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 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

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, and 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 and 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.

Hardcopy output to plotters and printers that support HPGL and PostScript.

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

Menu access for rapid, customized 1-D processing.

Matrix storage of two-dimensional (2D) data for easy access to t_₁ and t_₂ 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.

Stack plot for 3D display of 2D data.

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.

BioMagResBank deposition support.

Table interface to the database.

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

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.

Three dimensional intensity and contour plot displays with real-time rotation.

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_a-C_b 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_a, C_a, and C chemical shift libraries.

Tool for generating reports about the assignment of patterns.

Model module features

Back-calculation of 2D/3D NOESY spectra.

Complete pan and zoom display of the molecular coordinates.

Real-time rotations of molecular coordinates.

Coordinate cross peak footprints and parent nuclei.

Coordinated matrix display limits and cursors.

Molecular models may be displayed using vector or van der Waals spheres (adjustable radii).

Determine interatomic distances within the molecular coordinates.

Analysis interface compatible with IRMA simulations.

Flexible multi-window interface which can assemble experimental NOESY data, back-calculated data, and a molecular structure (coordinates) in an interactive environment.

Hot links to Insight II to display parent nuclei for cross peaks.

Autoscreen module features

Comprehensive features to organize a SAR by NMR-like project in a database.

Unlimited number of 2D ^¹⁵N-HSQC 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 more reliable peak matching and scoring.

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 K_{_d} 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 Cerius^² 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.

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^{^Ž} 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:

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 Insight interface are presented in bold type. For example:

Select the Model pulldown.

UNIX command dialog 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:

     > cerius2 -b output scriptfile

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.