Felix User Guide

How to Use This Book

The Felix book is a basic guide to working with the Felix software.

There are two ways to access this online book, either at our website (HTTP://www.msi.com/doc) or from the installed Insight II documentation CD ($MSIDOC). Keep in mind, though, that any updates or corrections will be posted to the web site, making the information at www.msi.com the most current.

Although an index and table of contents are provided, you are encouraged to make use of the searching capabilities of your browser to locate information.

This book is only available online. If you wish, you may print individual chapters of this guide using your browser's printing capability.

Please see the online help for more information about the commands 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

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

Topics covered

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® 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.

A complete NMR data processing and analysis program, Felix provides you with tools for efficiently transforming NMR data of almost any dimensionality and 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 the user to create their own menus and user interface, or to customize the existing menus.

The quantity and variety of data 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 the user to quickly store data temporarily or permanently in disk files, to display the data as lists, and to edit the spectral information using the table interface. The database also sorts data into lists according to user-defined criteria and can compare lists for similarities or differences.

Feature list

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 point(s) 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, or 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 plotting on plotters and printers that support HPGL and PostScript.

• Display features which 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 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.

• 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 which 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.

• 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 of 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.

• Comprehensive features to organize the assignment project in a database.

• Defines up to 12 spectra in one experiment.

• Overlays multiple contour plots in real time.

• Overlays multiple peak entries on contour plots.

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

• Displays 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.

• 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 is 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

There are now two methods for starting Felix. One method is to start Felix as a stand-alone program by typing the appropriate program name. See the MSI Products System Guide for a complete list of program names.

You may also start Felix from within Insight® II by clicking the MSI logo and selecting NMR_Refine from the resulting list. Once within the NMR_Refine module, select the Felix/Start_Felix command. After verifying that the correct executable file is listed in the resulting dialog box, select Execute. For further details on invoking Felix, and for tutorials, see the Felix Tutorials (these are located in a separate book).

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

Related 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 describes 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.

• Names of modules, pulldowns, command names, and names of things in the Insight interface are presented in bold type. For example:

  Select the Model pulldown.

• UNIX command dialog and file samples are represented in a courier font. If the dialog is something you must type, it is given in bold courier font. For example:

>	cerius2 -b output scriptfile

• In referring to the commands 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. In cases where there is more than one menu pulldown to access before the command name appears, the pulldowns are simply given in the order that you select them.