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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. 688-689
Section 25.1.4. Phase determination and structure solution
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 |
AMoRe
(Navaza, 1994![[link]](/graphics/greenarr.gif)
) is a program package that carries out structure determination using molecular replacement. It reformats the data from the new crystal form, generates structure factors from the model, calculates rotation and translation functions, and applies rigid-body refinement to the solutions. AMoRe is part of the CCP4 suite (Section 25.1.2.4).
Location: http://www.dl.ac.uk/CCP/CCP4/dist/html/INDEX.html . Operating systems: UNIX, VAM/VMS and LINUX. Type: source code and binary. Distribution: free academic.
GLRF
(Tong & Rossmann, 1990) is a program that calculates the general locked rotation function. The self-rotation function determines noncrystallographic symmetry in a crystal. The cross-rotation function determines the orientation relationship of a structure in one unit cell to similar structures in another cell. Since the relationship between the assumed molecular symmetry axes is `locked', the program can greatly enhance the signal peaks on the rotation function. Therefore, it is much more powerful for assemblies with high local symmetry, such as icosahedral viruses. GLRF is part of The Purdue University XTAL Program Library (PUXTAL: Section 25.1.2.9).
Location: http://www-structure.bio.purdue.edu/∼kvz/#GLRF . Operating system: UNIX. Type: source code and binary. Distribution: free.
The HEAVY program package contains the HEAVY and HASSP programs. The package can carry out heavy-atom search, refinement and MIR/MAD phasing. Some of the major features of HEAVY include correlated phasing, Bayesian weighting and Bayesian difference refinement.
Location: http://www.iucr.org/sincris-top/logiciel/prg-heavy.html or e-mail Ncameron@lanl.gov . Operating systems: UNIX and VMS. Type: binary. Distribution: free academic.
MADSYS
(Hendrickson, 1991) is a software package developed over the years in Dr Wayne Hendrickson's laboratory for determining experimental phases of macromolecular structures by multi-wavelength anomalous diffraction (MAD). The package consists of a set of programs that carry out MAD data handling, determination of anomalous-scatterer sites, refinement of MAD sites, MAD phases calculation and structure refinement.
Location: http://convex.hhmi.columbia.edu/hendw/madsys/madsys.html . Operating system: UNIX. Type: binary. Distribution: free academic.
MLPHARE
is a program for maximum-likelihood heavy-atom refinement and phase calculation. This program refines heavy-atom parameters and error estimates, then uses these refined parameters to generate phase information. The maximum number of heavy atoms that may be refined is 130 over a maximum of 20 derivatives. The program was originally written for MIR, but may also be used for phasing from MAD data, where the different wavelengths are interpreted as different `derivatives'. MLPHARE is part of the CCP4 suite (Section 25.1.2.4).
Location: http://www.dl.ac.uk/CCP/CCP4/dist/html/mlphare.html . Operating systems: UNIX, VAX/VMS and LINUX. Type: source code and binary. Distribution: free academic.
Shake-and-Bake
(SnB) (Weeks & Miller, 1999) is a program that uses a dual-space direct-methods phasing algorithm based on the minimal principle to determine crystal structures of macromolecules. The program requires very high resolution data to 1.2 Å or better and |E| values as input. SnB has been used to solve structures with more than 600 atoms in the asymmetric unit. Recently, SnB has also been used to determine the Se sites in large selenomethionyl-substituted proteins. See Chapter 16.1
for more details.
Location: http://www.hwi.buffalo.edu/SnB/ . Operating systems: UNIX, VMS and LINUX. Type: source code. Language: Fortran77. Distribution: free.
SHARP
(Statistical Heavy-Atom Refinement and Phasing; de La Fortelle & Bricogne, 1997) operates on reduced, merged and scaled data from SIR(AS), MIR(AS) and MAD experiments, refines the heavy-atom model, helps detect minor or disordered sites using likelihood-based residual maps, and calculates phase probability distributions for all reflections in the data set. See Chapter 16.2
for more details.
Location: http://www.globalphasing.com/sharp/ . Operating systems: IRIX and OSF1. Type: binary. Distribution: free academic.
References
Hendrickson, W. A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science, 254, 51.Google Scholar
La Fortelle, E. de & Bricogne, G. (1997). Maximum-likelihood heavy-atom parameter refinement in the MIR and MAD methods. Methods Enzymol. 276, 472–494.Google Scholar
Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Cryst. A50, 157–163.Google Scholar
Tong, L. & Rossmann, M. G. (1990). The locked rotation function. Acta Cryst. A46, 783–792.Google Scholar
Weeks, C. M. & Miller, R. (1999). The design and implementation of SnB version 2.0. J. Appl. Cryst. 32, 120–124.Google Scholar
