Refinement against order parameter with XPLOR

[nmrlearner]

New 2.10 release of XPLOR-NIH can now do a refinement against order parameters. You can get an idea what this refinement can be used for from the this paper.

Info about new features of XPLOR-NIH 2.10 from XPLOR-NIH website:

• - new parameter/topology file naming convention: NMR protein refinement should now use topology file protein.top and parameter file protein.par.
• - new command: tclXplor which calls xplor -tcl. Can be used as command interpreter
• - new potential term OrderPot to enable refinement against order parameters.
• - update to PrePot from Junji Iwahara
• - CSAPot: 15N CSAs are now supported.
• - hbdb update from Alex Grishaev: Adds ability use multiple segments. Includes fixes to prevent program crashes.

General information about XPLOR-NIH:

"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.
  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. "