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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 25.1, pp. 689-690
Section 25.1.6. Phase improvement and density-map modification
a
Biomolecular Crystallography Laboratory, CABM & Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA, and Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Yue-Yang Road, Shanghai 200 031, People's Republic of China, and bBiomolecular Crystallography Laboratory, CABM & Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA |
BUSTER
(Bricogne, 1997a![[link]](/graphics/greenarr.gif)
,b) is a program for recovering missing phase information by Bayesian inference. BUSTER has applications in maximum-likelihood refinement of partial structures in conjunction with the TNT program (Section 25.1.5.8), maximum-entropy structure completion for missing or ambiguous parts of a structure, and accurate electron-density reconstruction based on high-resolution X-ray diffraction data. BUSTER is related to SHARP (Section 25.1.4.7). See Chapter 16.2
for more details.
Location: http://www.globalphasing.com/buster/ . Operating systems: IRIX and OSF1. Type: binary. Distribution: free academic.
DM
(Cowtan, 1994) is a density-modification program package. DM applies real-space constraints based on known features of a protein electron-density map in order to improve the approximate phasing obtained from experimental sources. Various information can be applied, including the following diverse elements: solvent flattening, histogram mapping, multi-resolution modification, NCS averaging, skeletonization and Sayre's equation. DM is part of the CCP4 suite (Section 25.1.2.4). See Chapter 15.1
and Section 25.2.2
for more details.
Operating systems: UNIX, VAX/VMS and LINUX. Type: source code and binary. Distribution: free academic.
FINDNCS
(Lu, 1999) is a program that automatically determines NCS operations from heavy-atom sites to aid in applying averaging techniques in the MIR procedure. The program outputs the NCS operations (a rotation matrix and translation vector), r.m.s. deviations, polar angles and screw distance, matching sites and other useful information for users. The program can also generate files that can be used to display NCS operations using the program O (Section 25.1.7.7).
Location: http://www.ccp4.ac.uk/dist/html/findncs.html . Operating systems: UNIX, IRIX and OSF1. Type: binary. Language: Fortran77. Distribution: free academic.
RAVE
(Jones, 1992; Kleywegt & Jones, 1994) is a suite of programs for real-space electron-density averaging of crystallographic electron density between single and multiple domains, and between single and multiple crystal forms. It also contains tools for the detection of secondary-structure elements in macromolecular electron-density maps. See Chapter 17.1
for a detailed description.
Location: http://xray.bmc.uu.se/usf/menu.html#sof ; ftp://xray.bmc.uu.se/ . Operating systems: UNIX, SGI and DEC Alpha/OSF1. Type: binary. Distribution: free.
SOLOMON
(Abrahams & Leslie, 1996) is a program that modifies electron-density maps by averaging, solvent flattening and protein truncation. It can also remove overlapped parts of a mask between itself and its symmetry equivalents. SOLOMON is part of the CCP4 suite (Section 25.1.2.4).
Location: http://www.dl.ac.uk/CCP/CCP4/dist/html/solomon.html . Operating systems: UNIX, VAX/VMS and LINUX. Type: source code and binary. Distribution: free academic.
The SQUASH program (Zhang & Main, 1990a,b) provides a tool for phase refinement and extension of macromolecular structures. The starting point is a set of native structure factors to some resolution, and estimated phases and figures of merit for some subset of the phases. The result is a set of improved phases and figures of merit for the whole data set. The program combines Sayre's equation with density modification by histogram matching, solvent flattening and noncrystallographic symmetry averaging. The real-space formulation enables any electron-density constraint to be applied easily, e.g. solvent flattening with (eventually) known regions of density. The least-squares solution of a large system of nonlinear equations is achieved by Newton–Raphson iteration that converts the system of nonlinear equations into linear ones. The system of linear equations is solved by the conjugate-gradient method using FFTs.
Location: http://www.chem.ac.ru/Chemistry/Soft/SQUASH.en.html . Operating system: UNIX. Type: binary. Distribution: commercial.
References
Abrahams, J. P. & Leslie, A. G. W. (1996). Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst. D52, 30–42. Google Scholar
Bricogne, G. (1997a). Ab initio macromolecular phasing: a blueprint for an expert system based on structure factor statistics with built-in stereochemistry. Methods Enzymol. 277, 14–19.Google Scholar
Bricogne, G. (1997b). Efficient sampling methods for combinations of signs, phases, hyperphases, and molecular orientations. Methods Enzymol. 276, 424–448.Google Scholar
Cowtan, K. (1994). DM: an automated procedure for phase improvement by density modification. CCP4 ESF-EACBM Newsl. Protein Crystallogr. 31, 34–38.Google Scholar
Jones, T. A. (1992). A, yaap, asap, @#*? A set of averaging programs. In Molecular replacement, edited by E. J. Dodson, S. Gover & W. Wolf, pp. 91–105. Warrington: Daresbury Laboratory.Google Scholar
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Lu, G. (1999). FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy-atom sites. J. Appl. Cryst. 32, 365–368.Google Scholar
Zhang, K. Y. J. & Main, P. (1990a). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46, 41–46.Google Scholar
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