|
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. 687-688
Section 25.1.3. Data collection and processing
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 |
The Data Processing Suite (DPS) (Rossmann & van Beek, 1999![[link]](/graphics/greenarr.gif)
) is a complete package for processing X-ray diffraction data from crystals of proteins, viruses, nucleic acids and other large biological complexes. The emphasis is on diffraction data collected using synchrotron sources. Currently DPS consists of dps_index and dps_scale, and uses some of the programs from the MOSFLM/CCP4 suite. The dps_index program uses Fourier analysis for the automatic indexing of oscillation images. The dps_scale program uses a scaling method that does not depend on the exclusive use of full reflections. See Chapters 11.1
and 11.5
for more details.
Location: http://staff.chess.cornell.edu/∼szebenyi/DPS/ . Operating systems: UNIX, SGI and LINUX. Type: binary. Distribution: free academic.
The HKL program package (Otwinowski & Minor, 1996) is a complete set of data-processing programs for the analysis of X-ray diffraction data collected from single crystals. The package comprises three components: XDISPLAY for graphical visualization of the diffraction image; DENZO for autoindexing, reduction and integration of diffraction data; and SCALEPACK for scaling and merging of intensities from multiple images. See Chapter 11.4
for more details.
Location: http://www.hkl-xray.com/ . Operating systems: SGI, DEC Alpha, SUN and HP-UX. Type: binary. Distribution: commercial.
LOCSCL
(Blessing, 1997) is a program used to optimize statistically local scaling of single-isomorphous-replacement and single-wavelength anomalous-scattering data.
Location: e-mail blessing@hwi.buffalo.edu . Operating systems: UNIX and Windows. Type: source code. Language: Fortran77. Distribution: free.
MOSFLM
is a general-purpose data-processing package developed by Dr Andrew Leslie at the MRC, England. The programs have two main applications: (1) determination of crystal orientation, cell parameters and possible space group; and (2) autoindexing of images, generation of reflection lists and integration of diffraction spots. MOSFLM is distributed as part of the CCP4 suite and runs on multiple platforms. See Chapters 11.2
and 11.3
for more details.
Location: ftp://ftp.mrc-lmb.cam.ac.uk/ . Operating systems: UNIX and VAX/VMS. Type: source code and binary. Distribution: free academic.
The SCALA program (P. R. Evans, 1993, 1997) scales together multiple observations of reflections, and (optionally) merges multiple observations into an averaged intensity. Various scaling models are implemented. The scale factor is a function of the primary beam direction, either as a smooth function of φ (the rotation angle), or expressed as batch (image) number. In addition, the scale may be a function of the secondary beam direction derived from the spatial coordinates of the measured spot on the detector. In this case, the scaling is an interpolated three-dimensional function similar to that described by Kabsch (1988). The merging algorithm analyses the data for outliers and gives detailed analyses. It generates weighted means of the observations of the same reflection, after rejecting the outliers.
Location: SCALA is part of the CCP4 suite (Section 25.1.2.4). Operating systems: UNIX and VAX/VMS. Type: source code and binary. Distribution: free academic.
STRATEGY
(Ravelli et al., 1997) is a program that aids in designing data-collection strategy. It is used to determine the optimal starting spindle angle, using a one-circle diffractometer with a 2D detector, in X-ray data collection from crystals of macromolecules. The input file of the program contains information, from a DENZO intensities x-file, about starting crystal orientation and cell parameters. The program simulates all the reflections that can occur during 360° rotation of the crystal, determines if reflections can be recorded on the detector, sorts them, provides pictures of the needed oscillation range as a function of the starting spindle angle for given degrees of completeness of the data set and produces redundancy tables for the shortest data collection possible for each desired completeness. However, neither mosaicity nor overlaps are taken into account. This program has been integrated into the MOSFLM package (Section 25.1.3.4).
Locations: http://www.crystal.chem.uu.nl/distr/strategy.html ; ftp://ftp.chem.uu.nl/ . Operating system: UNIX. Type: binary. Distribution: free.
References
Blessing, R. H. (1997). LOCSCL: a program to statistically optimize local scaling of single-isomorphous-replacement and single-wavelength-anomalous-scattering data. J. Appl. Cryst. 30, 176–177.Google Scholar
Evans, P. R. (1993). Data reduction. In Proceedings of the CCP4 study weekend. Data collection and processing, edited by L. Sawyer, N. W. Isaacs & S. Bailey, pp. 114–122. Warrington: Daresbury Laboratory.Google Scholar
Evans, P. R. (1997). Scaling of MAD data. In Proceedings of the CCP4 study weekend. Recent advances in phasing, edited by M. Winn, Vol. 33, pp. 22–24.Google Scholar
Kabsch, W. (1988). Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Cryst. 21, 916–924.Google Scholar
Otwinowski, Z. & Minor, W. (1996). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326.Google Scholar
Ravelli, R. B. G., Sweet, R. M., Skinner, J. M., Duisenberg, A. J. M. & Kroon, J. (1997). STRATEGY: a program to optimize the starting spindle angle and scan range for X-ray data collection. J. Appl. Cryst. 30, 551–554.Google Scholar
Rossmann, M. G. & van Beek, C. G. (1999). Data processing. Acta Cryst. D55, 1631–1640.Google Scholar
