X-PLOR 98.0 - NEW FEATURES AND
ENHANCEMENT
Sándor Szalma, John Badger, R. Ajay
Kumar and Ping Yip
Molecular Simulations Inc., 9685 Scranton Road, San Diego,
CA 92121
X-PLOR 98.0 is a new release of the X-PLOR software from
Molecular Simulations Inc. containing important new features for
X-ray and NMR structure determination.
- Maximum likelihood technology (Pannu & Read, Acta
Cryst. A52, 659, 1996) for improved
refinement of macromolecular structures against amplitude
or intensity targets. A new maximum likelihood target,
which incorporates phase probability distributions to
make optimal use of all experimental information, is also
available.
- Andersen thermal coupling for temperature control during
simulated annealing. This method of thermal coupling
provides improved local conformational sampling, usually
leading to lower final values of Rfree, when used on
reasonably well-refined structures.
- A new utility program for converting reflection data from
a variety of arrangements to the X-PLOR format.
- Validated scripts for structure determination using NMR
distance restraints with torsion angle dynamics.
Optimization of the original torsion angle dynamics code
(Rice & Brünger, Proteins 19,
277, 1994) gives a speed-up of ~20% on these protocols
for a ~120 amino acid structure.
- Fast new code for Direct NOE Refinement. Matrix doubling
and Gaussian quadratures methodologies (Yip, J. Biol.
NMR, 3, 361, 1993) are implemented
and enhanced to achieve a substantial performance
improvement.
- Methodologies for using ambiguous restraint information
to perform automated iterative peak assignment and
structure determination (ARIA, Nilges et al., J. Mol.
Biol. 269, 408, 1997).
Graphical user interfaces to X-PLOR are provided through
InsightII/Xsight 97.0 for X-ray refinement and
InsightII/NMR_Refine and Felix 97.0 for NMR structure
determination.