Official government website icon

XPLOR-NIH

Current version: 3.9
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:

Linux/AMD64 binary is now compiled with Intel oneAPI compiler, and is significantly faster.
Added added example use of calcPRE helper in eginput/pre/calcPRE-example.
Optional OpenMP parallelization of energy terms in PotLists.
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.
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:

G. Marius Clore
Guillermo Bermejo,
John Kuszewski,
Charles D. Schwieters
Nico Tjandra

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)