| X-PLOR |
X-PLOR 98.0 builds on the interim version, X-PLOR 3.851, by providing significant enhancements and new applications for both X-ray crystallographic refinement and NMR structure determination. The major new features that were added to the X-PLOR distribution since the release of X-PLOR 3.1 are highlighted in the list below. The features added since the release of X-PLOR 3.851 are identified with an *.
The example scripts have been changed to reflect changes and additions to the X-PLOR command syntax, improved structure determination protocols, and the addition of standard libraries for space groups and atomic scattering factors.
Torsion angle dynamics, in which torsion groups within the molecule are kept completely rigid, increases the radius of convergence of crystallographic refinement by allowing simulated annealing at higher temperatures and with larger time steps (Rice and Brünger 1994). Torsion angle dynamics also has the benefit that it is more stable than conventional Cartesian dynamics and, since the number of degrees of freedom in the system is reduced, it is less prone to overfitting the data.
X-PLOR is now able to carry out MAD phasing applications including data scaling and merging, difference map calculations, refinement of the anomalous scatterer sites and phasing (Burling et al. 1995).
4. 
A-weighting for electron density maps with optional cross-validation
Improved electron density maps with reduced bias may be calculated using Aweights (Read 1986; Hodel et al. 1992) or cross-validated A weights. This facilitates model re-building.
5. Difference, anomalous difference, and <n>Fo-<m>Fc electron density maps
Example scripts are available for producing the types of electron density maps most commonly used in macromolecular crystallography.
A method
Scripts are included for estimating co-ordinate errors in macromolecular structures from the calculation of Luzzati (Luzzati 1952) and A (Read 1986; Kleywegt and Brünger 1996) plots.
7. Script files for molecular replacement with multiple molecules
Example scripts are provided for carrying out molecular replacement searches for the case where there are multiple molecules in the crystal asymmetric unit.
X-PLOR now allows picking water peaks (corresponding to ordered solvent molecules) from the region of the solvent that is close to the protein surface and writing out the solvent co-ordinates. An example script is provided for this application.
A procedure (including an example script) for creating a bulk solvent model (Jiang and Brünger 1994) and writing partial structure factors for this model is now included. With this procedure it should be possible to include all of the very low-resolution structure factor data in refinement and map calculations.
The command syntax is now expanded to explicitly support the direct rotation function. In this rotation function the search molecule is placed in a crystal cell with the same dimensions as the unknown crystal and the rotation function is computed for the molecule systematically placed in different rotations (DeLano and Brünger 1995). This brute force rotation function is accurate but computationally expensive.
11. Phased translation function
The phased translation function is able to use the extra (phase) information that is available for locating the translational components of a trial model when, for example, phase information has been obtained from a heavy atom derivative. The algorithm searches for maximum correlation of observed and calculated electron densities (Read and Schierbeek 1988).
12. X-PLOR -> PDB deposition script (for crystal structures)
A script is provided that sets up some of the information on the refined structure so you can use automated input through the electronic deposition system at the Brookhaven Protein Data Bank.
This program takes structure factor data in a variety of formats and prepares a data file for use with the X-PLOR format. This more generic program replaces the Scalepack/Denzo-to-X-PLOR conversion program provided with X-PLOR 3.851.
The maximum likelihood targets for the refinement of macromolecular models provide much more convergent and reliable results than the conventional residual target, particularly when the model is incomplete and relatively inaccurate (Pannu and Read 1996; Adams et al. 1997). Since the computational cost of ML refinement is little different from conventional refinement, the intensity-based ML target is now standard (default). Scripts are provided illustrating the use of the ML targets.
15. *Andersen thermal coupling
The Andersen thermal coupling method (Andersen 1980) has been adapted for use with the simulated annealing code within X-PLOR. The Andersen thermal coupling method appears to give better local sampling than Berendsen thermal coupling and most structures refine to slightly better (~0.5%) Rfree values if the Andersen thermal coupling method is used in the final stages of simulated annealing refinement.
1. Time- and ensemble-averaged NOE distance restraints
New features for NMR structure determination
In structure determination by X-ray crystallography and solution NMR spectroscopy, experimental data are collected as time- and ensemble-averages. Thus, in principle, appropriate time- and ensemble-averaged models should be used. For refinement with time-averaged NOE distance restraints (Torda et al. 1989, 1990; Pearlman and Kollman 1991) the NOE restraint potential is changed so that distance restraints derived from NOE are applied to the time-average of each distance, rather than each instantaneous distance. With ensemble-averaging, an ensemble of conformers rather than one single structure is used to satisfy the experimental NMR data (Bonvin and Brünger 1996).
2. Cross validation of NOE distance, NOE intensity, and dihedral angle restraints
The idea of cross-validation for structure determinations involving NOE distance, NOE intensity, and dihedral angle restraints (Bonvin and Brünger 1995) is illustrated by the scripts used for ensemble averaging.
3. J-coupling and proton and carbon chemical shift refinement
Direct refinement against three-bond HN-CaH coupling constants (Garrett et al. 1994) is now available.
Direct proton chemical shift refinement (Kuszewski et al. 1995a, 1996) and direct secondary carbon chemical shift refinement (Kuszewski et al. 1995b, 1996) are also available and exemplified by tutorial scripts.
4. *Ambiguous restraints and iterative assignments: ARIA
Methodologies for using ambiguous restraint information to perform automated iterative peak assignment and structure determination (Nilges 1997) are implemented in X-PLOR 98.0 and a set of tutorial files is provided.
5. *Structure calculation with torsion angle dynamics
Torsion angle dynamics provides an efficient method for NMR structure determination, with a high success rate when compared to conventional methods (Stein et al 1997). An example script is provided for NMR structure determination using this protocol. The Stein et al. protocol involves the use of both torsion angle and Cartesian dynamics. A sample protocol is also provided for NMR structure determination that uses only torsion angle dynamics.
The torsion angle algorithm (Rice and Brünger 1994) has been recorded in more computer-efficient form giving a saving (depending on the size of the structure) of ~20% on the total run time for these protocols.
6. *Fast direct NOE intensity refinement
A new methodology for computing NOE intensities and gradients has been incorporated into this version of X-PLOR. This new technique is based on the Matrix Doubling and Gaussian Quadrature approximation (Yip 1993). The increase in speed over methods available in previous versions of X-PLOR spans one to two orders of magnitude.