XPLOR-NIH

Current version: 3.10
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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:

• Fixed the mmCif reading code so that AlphaFold .cif files are now read correctly.
• Added missing ISOP (isopeptide) patch to the default parameters.
• Added the evalCovalent helper program to quickly list covalent violations.
• PASD automatic assignment facility:
  • - Added better support for input formats sparky, xeasy
  • Reimplemented much of jointFilter in C++ with OpenMP parallelization - it is now much faster.
  • Switched to Python versions of the scripts for the PASD/cvn example.
• eginput/PSF_generation/genLigandCif.py: better support for generating parameters non-standard protein residues (from an appropriate wwPDB ligand .cif file).
• python/varTensorTools.py: calcTensorOrientation reimplemented in C++ using non-linear least square optimization.
• 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.
  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
• 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)

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