Current version: 2.42
New in this release:
XPLOR-NIH is a structure determination program which builds on the
program, including additional tools developed at
the NIH. These tools include functionality for the following:
eginput/rna: a full example using the new RNA-ff1 for better RNA structures
the HBDB term: lifted the (silent) limitation of having 10 unique segids
added repelPot: a C++ implementation of XPLOR's REPEl nonbonded
term. Easier to apply term to subsets of atoms within a
structure, and more accurate violation reporting. An example of
use can be found in eginput/gb1_rdc/anneal2.py
- Many bug fixes, documentation improvements, optimizations and
other additions. Please see the
- 3J couplings
- 1J couplings
- 13C shifts
- 1H shifts
- dipolar couplings
- radius of gyration
- 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
- embedded Python and TCL interpreters.
- addition of Generalized Born code from Tom Simonson .
- support for computing swarms of structures in parallel using
- 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.
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:
G. Marius Clore
, Guillermo Bermejo,
, John Kuszewski,
Charles D. Schwieters, and
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 are listed
. Please cite all appropriate references.
Please see the documentation page.
Here is a frequently asked questions page:
For questions about this package, please use the
mailing list. Archives of answered questions can be found
To download XPLOR-NIH binary packages or source code, please click
. Instructions for installation of these packages can be found
The following are available:
To be notified when new versions of XPLOR-NIH are released, subscribe
mailing list by sending a message to xplor-NIHfirstname.lastname@example.org.
- 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
To obtain the source code of XPLOR-NIH please contact either
Charles Schwieters (Charles.Schwieters@nih.gov)
Marius Clore (email@example.com)
Tools for use at NIH.
National Institutes of Health
Department of Health and Human Services