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XPLOR-NIH

XPLOR-NIH

Current version: 3.11.1
Download. Documentation. FAQ. Support. Training.

Xplor-NIH versions 3.0 and later are based on Python 3. Scripts in the eginput subdirectory have been updated to work with this version. Old user scripts should be *mostly* compatible with the new version, the primary cause for problems being the print statement, which is now a function requiring parentheses. So print "value" should now be print("value") .

New in this release:

  • Version 3.11.1 contains a fix important for installations where users do not have write permission to the install directory.
  • The bin/pip command is now included to ease installation of additional packages.
  • Added the -pyprof option to bin/xplor - perform profiling of Python scripts.
  • Added examples of 2D EM projection manipulation.
  • PASD: added support for pseudo-4D spectra (CNH, NCH, CCH, NNH).
  • Added Zinc-finger PSF generation examples.
  • Implementation of DSSP secondary structure algorithm in the new dssp module.
  • IVM - added rotate1 and translaterotate1 hinge types for constrained rigid-body motion.
  • PDBTool - added compatibility with more mmCIF files.
  • New energy term VecPairOrientPot to restrain angles between vectors defined by two pair of atom selections.
  • OpenMP support (using the -omp flag) now is enabled on the Darwin arm64 (Mac Arm) platform.
  • Many bug fixes, documentation improvements, optimizations and other additions. Please see the changelog.

XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH. These tools include functionality for the following:
  • 3J couplings
  • 1J couplings
  • 13C shifts
  • 1H shifts
  • T1/T2
  • dipolar couplings
  • radius of gyration
  • CSA
  • solution X-ray and neutron scattering
  • refinement using paramagnetic relaxation enhancement spectroscopy
  • conformational database torsion angle potentials
  • database base-base positioning potentials for DNA
  • interface to the NMR graphics package VMD-XPLOR, downloadable separately.
  • embedded Python and TCL interpreters.
  • addition of Generalized Born code from Tom Simonson .
  • support for computing swarms of structures in parallel using multiple computers.
  • paramagnetic relaxation enhancement module (Python interface) based on the modified Solomon-Bloembergen equation and multiple structure representation for paramagnetic groups. This module contributed by Junji Iwahara. Please contact him at iwahara-at-helix.nih.gov(replace -at- with a @) for further information.
  • The PASD/Marvin facility for automatic NOE assignment.
  • the PARArestraints module for including paramagnetism-based NMR restraints in refinement.
  • the bin/seq2psf script to generate psf file from sequence.
  • includes the isac code for floating RDC alignment tensor.
      H.J. Sass, G. Musco, S.J. Stahl, P.T. Wingfield and S.Grzesiek, J. Biomol. NMR 21: 275-280 (2001).
  • merged hbdb code from A. Grishaev. An empirical pseudo-potential that encodes for the relative arrangement of two protein peptidyl units linked by a backbone-backbone hydrogen bond.
  • a new CSA potential in the Python interface.
  • Removed arbitrary limits on all PSF parameters. Xplor-NIH startup size has been reduced by about 25MB, and it will handle systems as large as your computer's memory will allow.

XPLOR-NIH also includes an new internal variable module (IVM) which allows one to perform efficient molecular dynamics and minimizations using internal coordinates, such as torsion angles. The IVM permits one to do combined torsion angle/rigid body dynamics, torsion angle/cartesian coordinate dynamics, etc. We have found that a 6th order predictory-corrector integrator utilizing a time-varying, automatically time step size provides large computational advantages over the other X-PLOR dynamics engines.

Authors of the NIH extensions:

When publishing work which utilizes Xplor-NIH, please cite:

  • C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore, "The Xplor-NIH NMR Molecular Structure Determination Package," J. Magn. Res., 160, 66-74 (2003).
  • C.D. Schwieters, J.J. Kuszewski, and G.M. Clore, "Using Xplor-NIH for NMR molecular structure determination," Progr. NMR Spectroscopy 48, 47-62 (2006).
Other relevant references . Please cite all appropriate references.

Documentation

Please see the documentation page. Here is a frequently asked questions page: FAQ.

Support

For questions about this package, please use the Xplor-NIH mailing list by sending a message to xplor-nih@list.nih.gov. Archives of answeared questions can be found at https://list.nih.gov/cgi-bin/wa.exe?A0=XPLOR-NIH . To obtain the source code of XPLOR-NIH please contact either
Charles Schwieters (Charles.Schwieters@nih.gov)
or
Marius Clore (mariusc@intra.niddk.nih.gov)