Programs are listed sequentially, according to the normal order of use in a typical NMR structure determination project. Rather than providing detailed tutorials on the use of the various programs, a few comments on the general use of each program are provided, as well as the literature citations and links to the original documentation.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol | modelfreebruk2pipe: Converts AMX and DMX ser files (raw NMR data) to the nmrPipe format for subsequent processing (FT) by nmrPipe. Use the handy bruker GUI to automatically generate a conversion script customized for your nD NMR experiment (a similar script generator for Varian data is also available, but we have not used it). While in a directory containing all your acquisition files from the spectrometer (acqus, ser, pulseprogram, etc.), type 'bruker' to start the program. Press the 'read parameters' button, make adjustments to any values that might be incorrect (it gets the two indirect dimensions of a 3D confused sometimes, for instance), and then press the 'save script' button to write the file 'fid.com'. Important tip: Before executing it, make two corrections to the fid.com file. 1 Change the first line from '#!/bin/csh' to '#!/bin/sh'. 2 On the 'bruk2pipe' line substitute '-noaswap' for '-noswap' to account for big-endian vs. little-endian data formats on Linux and other Unix environments (the -noaswap flag is an update which determines the local data format and automatically does byte-swapping but only if necessary). Example fid.com for converting a 2D 15N HSQC dataset.
Availability:Comes with nmrPipe.
Literature Citation: See nmrPipe below
Original Documentation:
Provided as Unix man pages; type 'man bruk2pipe'; if no entry is found, make sure your MANPATH environment variable includes the nmrPipe man directory (e.g. /usr/local/lib/nmrpipe/man)
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol | modelfree
- nmrPipe: A system for the complete processing of multidimensional NMR spectra, including functions for Fourier transformation, phasing, apodization, baseline correction, linear prediction, and others, developed by and available from Frank Delaglio at the NIH. Typical processing schemes utilize a shell script which executes a series of individual nmrPipe commands simultaneously, with the output of one command providing input directly to the next command. Each nmrPipe command performs a single specific operation (FT, phase correction, etc.) on all the vectors along one dimension of the N-dimensional dataset. To achieve a complete 2D or 3D FT, the dataset is transposed after execution of one FT (i.e. X- and Y-dimensions are exchanged) and a second FT is applied to the transposed vectors. Because all spectral parameters are provided in the header of the input data (this information is incorporated automatically in the bruk2pipe conversion step - see above), including the time-domain data sizes of each dimension, very few parameters need adjustment within the nmrPipe script for a given type of NMR experiment. Example nmrproc.com for processing a 2D 15N HSQC spectrum. The program nmrDraw, provided with the nmrPipe package, provides a tool for examining nD data in nmrPipe format, and is especially useful for obtaining phase parameters for use in nmrPipe processing.
Availability:
A Linux executable is available. Contact Frank Delaglio directly for further information.Literature Citation:
F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax, J. Biomol. NMR, 6 (1995) 277-293. An HTML version is of the paper is also available.Original Documentation:
Provided as Unix man pages; type 'man nmrPipe'; if no entry is found, make sure your MANPATH environment variable includes the nmrPipe man directory (e.g. /usr/local/lib/nmrpipe/man). A nice resource for nmrPipe documentation and sample scripts can be found at Rachel Klevit's web site (Univ. of Washington). NMRFAM users can access an HTML version of the nmrPipe man pages on the NMRFAM Extranet: Browse through the Workstations section to the listing of software installed on NMRFAM computers to find a link to the nmrPipe documentation. This section of the NMRFAM web site is restricted to authorized users, however.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol | modelfree- spscan: Our primary use has been for the conversion of nmrPipe format processed data to the xeasy submatrix format. Use the macro pipe2xeasy_a.spm to convert any 2D or 3D nmrPipe dataset into xeasy format. spscan can be run directly from the command line in a batch mode with the '-m' flag, or this conversion can be incorporated directly into an nmrPipe processing script as shown in this example. When this script is successfully executed, the HSQC is processed by nmrPipe, written out in nmrPipe format (test.ft2) and also converted to xeasy format (test.3D.16). The 'showhdr' command generates the long-format nmrPipe header file that spscan needs to perform the conversion, and the spscan line runs spscan with the pipe2xeasy_a.spm macro as input. The primary drawback to data conversion with spscan is that even when executing the macro, spscan prompts the user with GUI pop-up windows, and starts the spscan menu interface upon completion. An X-windows environment must therefore be available when running the spscan conversion; if the program is being run remotely, make sure that the remote computer is allowed to display on the local X server (xhost +) and that the display is set to the local host (setenv DISPLAY localhost:0.0). In addition, minor problems with the conversion of some 3D datasets to XEASY have been described, with a simple-minded solution, in the linuxnmr@nmrfam.wisc.edu mailing list.
Availability:
Contact Ralf Glaser as directed on the spscan home page. A Linux executable is available.Literature Citation: none yet.
Original Documentation:
The spscan homepage has an online manual.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol | modelfree
- xeasy: This is a graphical interface for multidimensional NMR data after it has been processed. Spectra can be peakpicked either manually or automatically with XEASY, and multiple integration modes are available. It provides a wide range of tools for sequential assignments with either NOESY/TOCSY data (2D or 3D) or backbone triple-resonance experiments. Generating strip plots of 3D spectra is a very simple process in XEASY. A fully automated assignment scheme is not included in XEASY (see instead GARANT), but a method for tabulating chemical shifts and peak assignments is used which provides complete compatibility with the structure calculation program DYANA.
Availability:
Academic licenses are available for US$200.Literature Citation:
Ch. Bartels, T.-H. Xia, M. Billeter, P. Güntert and K. Wüthrich (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomolecular NMR 5, 1-10.Original Documentation:
The XEASY homepage and XEASY manual are available online. The table of contents is a useful reference, as it lists the command names with the two-letter codes for each, grouped by topic (peak picking, assignment, etc.). Look at the various tutorial-style examples for instructions on specific assignment tasks (e.g. NOESY/TOCSY, HNCA/HNCOCA, etc.)
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol| modelfree- Sparky: A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers, Sparky may eventually replace XEASY for our spectral peakpicking and assignment tasks, but it has not been used in that capacity by us yet. We are adopting Sparky to take advantage of a new python extension for analysis of 15N relaxation data. This new feature automates the extraction of peak intensities and exponential fitting of a series of 2D HSQC-type spectra to obtain T1 or T2 values. These tools can also be used for fitting other types of decay data, such as NH exchange for determining protection factors. The newest versions of Sparky, v. 3.70 and later, include these features.
Availability:
Download a trial version (good 'til 4/9/2000), or buy a $200 permanent license.Literature Citation:
None (as far as I can tell).Original Documentation:
Full documentation is provided, including an online manual. If you want to print the manual there is a Postscript version with links replaced by page references.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | nmrview | garant | dyana | molmol| modelfree
- NMRView: Another software tool for the visualization and analysis of NMR data, NMRView may represent a very good choice for the Linux platform, but we have not taken the opportunity to experiment with it yet. Curt Hastings at UC Berkeley has documented his efforts with NMRView and other software in Linux, including his own value-added NMRView distribution. NMRView is notable for the fact that it is completely free, under active development by Bruce Johnson (Merck), easily customized and extended using Tcl/Tk, and available for a very wide range of platforms, including the MacOS. Read more of Curt Hastings' perspective on NMRView in the LinuxNMR mailing list or post your own. Thanks go to Curt for providing the spiffy screenshot of his NMRView distribution at work (even though it appears to be running under Irix).
Availability:
Download the latest version (4.1.2) from NMRView.com.
Download the Berkeley distribution from Curt Hastings' web site.Literature Citation:
B. A. Johnson and R. A. Blevins, (1994) NMRView: A computer program for the visualization and analysis of NMR data, J. Biomol. NMR 4 603-614.Original Documentation:
Full documentation is provided, including an online manual. The NMRView mailing list provides additional technical support.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | garant | dyana | molmol | modelfree- garant: GARANT is an algorithm for automatic resonance assignment using as input the primary structure of a protein and lists with observed cross peaks from various spectra; knowledge about magnetization transfer pathways in the NMR experiments used is read from a library. The basic concept of GARANT is the matching of observed cross peaks to expected cross peaks derived from the sequence and the magnetization transfer pathways. I have heard reports of very good performance from this program; I have not been so successful in my attempts to use it for assignment of 3D NOESY spectra. I hope to test it on triple resonance spectra for obtaining resonance assignments sometime in the near future, and will update these notes if I have any success.
Availability:
Download Garant 2.0 from the Wüthrich lab web site.Literature Citation:
C. Bartels, P. Güntert, M. Billeter and K. Wüthrich, J. Comp. Chem., 18, 139-149 (1997). GARANT - a General Algorithm for Resonance Assignment of Multidimensional Nuclear Magnetic Resonance Spectra.C. Bartels, M. Billeter, P. Güntert and K. Wüthrich, J. Biomol. NMR, 7, 207-213 (1996). Automated Sequence-specific Assignment of Homologous Proteins using the program GARANT.
Original Documentation:
A tutorial and example files provided with Garant 2.0 are probably the best resources for getting started with the program.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | garant | dyana | molmol | modelfree
- dyana:Torsion angle dynamics calculations of protein and nucleic acid structures from NMR-derived restraint data (NOE, J-coupling, torsion angles, dipolar couplings, chemical shfits), written by Peter Güntert in the Wuthrich lab at the ETH, Zurich (read a comprehensive introduction in his own words). I have used DYANA to determine a number of protein structures (e.g. PSP1 and a plastocyanin). I have been most impressed with both the computational speed and the ease of use of dyana, in comparison with X-PLOR, which I used for two protein structure determinations previously. One simple shell script is sufficient to specify all the parameters and commands for a complete torsion angle dynamics calculation. dyana takes as input the same files used and generated by xeasy (sequence, chemical shift list, NOESY peak list) and automatically generates distance restraints using the 'caliba' function. Routines for the assignment of NOESY peaks based on chemical shift matching and comparison with structure (assign) as well as automated iterative structure refinement (noah) are incorporated into dyana, and peak lists which have been assigned by dyana (or garant) can be read back into xeasy for visual inspection or modification.
Availability:
Academic licenses for DYANA that include the source code are available for US$ 200. The current version is 1.5. Compiling DYANA to run on properly on your Linux machine is not completely trivial, as described on the LinuxNMR Development page.Literature Citation:
Güntert, P., Mumenthaler, C. & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298.Original Documentation:
The DYANA manual is available in PDF format from the DYANA homepage. In addition, users can participate in a DYANA mailing list, where many common questions have already been asked and answered.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | garant | dyana | molmol | modelfree
- molmol: Molmol is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95 and is freely available. Molmol was developed in the Wüthrich lab at the ETH, Zurich, by Reto Koradi. Molmol contains a n r o atures geared toward the display and analysis of the structural ensembles generated from NMR data. Molmol reads and writes pdb, .ang torsion angle and .cor coordinate formats used by dyana as well as dyana restraint files. It can generate high-quality rendered Images in a variety of popular file formats, and can generate POV-RAY input files for advanced scene rendering with POV-RAY software.
Availability:
Download a Linux x86 binary of Molmol from the Wüthrich lab (molmol-2.6.0-bin-lnx.tar.gz) or Kevin Gardner's mirror site in the US (molmol-2.6.0-bin-lnx.tar.gz), or the source code (ETH or US). We are still working on compiling fully functional versions of MOLMOL from the source, but the binary provided by the authors seems to work fine. Hopefully we will soon be able to take advantage of 3D graphics acceleration harware soon to be widely supported under Linux, as described on the LinuxNMR Development page.Literature Citation:
Koradi, R., Billeter, M., and Wüthrich, K. (1996) J. Mol. Graphics 14, 51-55. MOLMOL: a program for display and analysis of macromolecular structures.Original Documentation:
The manual in PDF format is distributed with the program, but is also available in HTML at the molmol homepage, where you can also find the molmol mailing list archives and much information about obtaining molmol for a variety of platforms (including useful tips for Linux installation). Most useful for gaining familiarity with the somewhat difficult command line syntax are the tutorial examples.
bruk2pipe | nmrPipe | spscan | xeasy | sparky | garant | dyana | molmol | modelfree- modelfree: Modelfree is a program written by Prof. Arthur G. Palmer (Columbia University) for optimizing "Lipari-Szabo model free" parameters to heteronuclear relaxation data. The current version is 4.01. We have obtained the source for Model-Free in order to generate a Linux x86 binary; this executable is available from Prof. Art Palmer's web site.
Availability:
Download a Linux x86 distribution of ModelFree 4.01 from the Palmer lab web site, or get the source code by contacting Art Palmer directly.Literature Citation:
Mandel, A.M., Akke, M., & Palmer, A.G. (1995) J. Mol. Biol. 246, 144-163, Backbone Dynamics of Escherichia coli Ribonuclease HI: Correlations with Structure and Function in an Active Enzyme.Original Documentation:
The manual in PDF format is online at the Palmer Lab web site. First-time ModelFree users should consult the Mandel et al. JMB paper noted above for a detailed discussion of the model selection process. Additional notes on model-selection strategies at the Palmer lab web site are also very useful. A set of scripts, macros and curve-fitting programs by Art Palmer and Mikael Akke are also available from the Palmer lab.
