Utilities

Kleywegt, G. J.; Zou, J.-Y.; Kjeldgaard, M.; Jones, T. A.

doi:10.1107/97809553602060000691

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 17.1, pp. 355-356

Section 17.1.5. Utilities

G. J. Kleywegt,^a J.-Y. Zou,^a M. Kjeldgaard^b and T. A. Jones^a ^*

^aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden, and ^bInstitute of Molecular and Structural Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
Correspondence e-mail: alwyn@xray.bmc.uu.se

17.1.5. Utilities

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Many utility programs are available from Uppsala, most of them aimed at practising crystallographers. Some of these (MAMA, MAPMAN, DATAMAN) have been discussed in Section 17.1.3. A few others are discussed below.

(1) LSQMAN (Kleywegt & Jones, 1997b; Kleywegt, 1996). This is a program for analysing and manipulating multiple copies of a molecule or multiple molecules. It contains tools to superimpose molecules (including an option to find such superpositioning automatically), to improve the fit of two superimposed molecules in myriad ways, to calculate and plot r.m.s. distances and $[\varphi, \psi]$ or $[\chi_{1}, \chi_{2}]$ torsion-angle differences and circular variances (Allen & Johnson, 1991; Korn & Rose, 1994; Kleywegt, 1996) of different molecules, to generate multiple-model Ramachandran plots, to compare the solvent structure in two molecules, to find the `central' molecule of an ensemble [defined as the molecule that has the smallest r.m.s.(r.m.s.d.), i.e. the r.m.s. value of its pairwise r.m.s.d.'s to each of the other molecules], and to align molecules in an ensemble to the `central' molecule. The program can handle proteins, nucleic acids and other types of molecules.
(2) MOLEMAN2. This is a general program for analysis and manipulation of molecules (in PDB-format files). It contains too many options to list here, including tools that are of use when submitting structures to the PDB, several options that interface with O, X-PLOR (Brünger, 1992b), CNS (Brünger et al., 1998) and CCP4 (Collaborative Computational Project, Number 4, 1994), tools to analyse and manipulate temperature factors and occupancies, simple validation tools for protein models [e.g. Ramachandran (Kleywegt & Jones, 1996c) and Cα-Ramachandran plots (Kleywegt, 1997)], and simple distance and sequence analysis options.
(3) ODBMAN. This is a program for analysis and manipulation of O-style data blocks, offering a superset of the functionality available in O itself for this purpose. Data blocks can be plotted, combined, generated etc.
(4) OOPS2 (Kleywegt & Jones, 1996b). This program uses the current model and quality-related properties calculated in O or by OOPS2 or external programs to produce a detailed account of the quality of the model and the individual residues, and to generate a set of macro files for O that will take the crystallographer to all the residues that are outliers for one or more of the quality criteria.
(5) SEAMAN. This program offers several tools to help the crystallographer generate search models for use in molecular-replacement exercises. It is designed to handle `multiple search models' (e.g. an ensemble of NMR structures) as easily as single models.
(6) SOD. This program produces various types of file for use with O, based on aligned amino-acid sequences. For instance, it can generate data blocks and macro files that can be used to colour a protein model according to the degree of conservation or variability of each residue, or it can be used to generate an O macro file that will `mutate' an existing protein model into a molecular-replacement probe for a related protein.
(7) XPLO2D. This program was written to perform various functions for users of the refinement program X-PLOR (Brünger, 1992b). Its most useful component is the option to generate topology and parameter files automatically [for use with X-PLOR, CNS (Brünger et al., 1998), TNT (Tronrud et al., 1987), or O] for hetero entities based on the coordinates of one or more copies of such an entity.

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International Tables for Crystallography (2006). Vol. F. ch. 17.1, pp. 355-356