Hasil untuk "Crystallography"

C. P. Brock

P. Afonine, B. Poon, Randy J. Read et al.

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps. Synopsis A description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.

B. Toby, R. Dreele

A. L. Spek

This paper reports on the current status of structure validation in chemical crystallography.

Vincent B. Chen, W. B. Arendall, J. Headd et al.

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction.

L. Farrugia

Axel T. Brüngera, Paul D. Adamsb, G. M. Clorec et al.

Paul D Adams, P. Afonine, G. Bunkoczi et al.

Collaborative Computational

A. Brunger

H. Berman, Tammy Battistuz, T. N. Bhat et al.

N. F. M. Henry, K. Lonsdale, J. Kasper et al.

A. W. Schüttelkopf, D. V. van Aalten

The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG-generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors.

Philip R. Evans

E. Krissinel, K. Henrick

L. Barbour

P. Adams, R. Grosse-Kunstleve, Li-Wei Hung et al.

J. Agirre, Mihaela Atanasova, Haroldas Bagdonas et al.

This article describes the Collaborative Computational Project No. 4 (CCP4). It is intended as a general literature citation for the use of the CCP4 software suite in structure determination.

A. Vaitkus, Andrius Merkys, S. Gražulis

Data curation practices of the Crystallography Open Database are described with greater focus being placed on the cif_validate program, capable of validating crystallographic information files against both DDL1 and DDLm dictionaries.

David Richardson