XPLOR-NIH
Current version: 2.33
download.
documentation.
FAQ.
Support.
Training.
New in this release:
-
bin/contactMap:
a new helper script to visualize molecular contacts.
- bin/ramaStrip:
a new helper script to help quickly visually evaluate Ramachandran
quality of a large number of structures. Based on torsionDBPot.
- torsionDBPot:
better reporting of per-structure, average statistics for this term.
- updates to the bin/pbsxplor helper script so that it now
supports PBSPro on large single system image machines, notably the
SGI Altix.
- problem using the -smp option on some platforms has been
resolved.
- Many bug fixes, 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:
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).
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
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 use the
xplor-nih@nmr.cit.nih.gov
mailing list. Archives of answered questions can be found
here
.
Availability
To download XPLOR-NIH binary packages or source code, please click
here
. Instructions for installation of these packages can be found
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 (mariusc@intra.niddk.nih.gov)
Tools for use at NIH.
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National Institutes of Health
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Department of Health and Human Services
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