Xplor-NIH versions 3.0 and later are based on Python3. 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
should now be
New in this release:
Protein-4.0 parameters based on those of CNS are now the default.
Many updates and improvements to the eginput/pasd/nef example.
New ability to perform calculations with an ensemble of
Many bug fixes, documentation improvements, optimizations and
other additions. Please see the
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:
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.
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.