XPLOR-NIH

Xplor-NIH is now based on Python3. This version is built using Python3.7, and also validated using Python3.8 and Python 3.9 (where it produces somewhat different output). Scripts in the eginput subdirectory have been updated to work with Xplor-NIH version 3. 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:

• Further improvements to the eginput/PSF_generation/genLigandCif.py script for generating topology and parameter input for small molecules.
• Added support for the following residue variants: SEP, TPO and PTR to the standard Xplor-NIH force field.
• Generalized the coarse-grain representatiion facility globDiffPotTools.
• NMR Exchange Format (NEF) support: added ability to handle RDCs.
• Added facility to auto-determine the set of ordered residues used for final fitting in simulationTools.StructureLoop.
• Many bug fixes, documentation improvements, optimizations and other additions. Please see the changelog.

• 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).

Documentation

Support

Availability

• executables for multiple Unix platforms.
• various useful parameter and topology files for proteins, dna and dipolar couplings.
• the various databases.
• some examples using most of the refinement tools, IVM torsion angle dynamics, etc. Additional examples are available here .

To obtain the source code of XPLOR-NIH please contact either

Tools for use at NIH.

National Institutes of Health

Department of Health and Human Services