XPLOR-NIH

Current version: 2.9.7. download. updates.

New in this release:

new documentation page
new script: pdf2psf to help with psf generation.
new architecture supported: native support for AMD64.

Here is a more complete list of changes.

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
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 , John Kuszewski, Charles D. Schwieters, and 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). Other relevant references are listed here . 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 send a message to xplor-nih@nmr.cit.nih.gov . Archives of answered questions can be found here .

Availability

To download XPLOR-NIH binary packages or source code, please click here . The following are available:

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 be notified when new versions of XPLOR-NIH are released, subscribe to the xplor-NIH-annouce mailing list.

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

Charles Schwieters (Charles.Schwieters@nih.gov)
or
Marius Clore (clore@speck.niddk.nih.gov)

Tools for use at NIH.