Chapter

Chapter 25.2 Programs and program systems in wide use

Crystallography of biological macromolecules

First Online Edition (2006)

Part 25. Macromolecular crystallography programs

  1. W. Furey1,
  2. K. D. Cowtan2,
  3. K. Y. J. Zhang3,
  4. P. Main4,
  5. A. T. Brunger5,
  6. P. D. Adams6,
  7. W. L. DeLano7,
  8. P. Gros8,
  9. R. W. Grosse-Kunstleve6,
  10. J.-S. Jiang9,
  11. N. S. Pannu10,
  12. R. J. Read11,
  13. L. M. Rice12,
  14. T. Simonson13,
  15. D. E. Tronrud14,
  16. L. F. Ten Eyck15,
  17. V. S. Lamzin16,
  18. A. Perrakis17,
  19. K. S. Wilson18,
  20. R. A. Laskowski19,
  21. M. W. MacArthur20,
  22. J. M. Thornton21,
  23. P. J. Kraulis22,
  24. D. C. Richardson23,
  25. J. S. Richardson23,
  26. W. Kabsch24,
  27. G. M. Sheldrick25

Published Online: 1 JAN 2006

DOI: 10.1107/97809553602060000724

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Furey, W., Cowtan, K. D., Zhang, K. Y. J., Main, P., Brunger, A. T., Adams, P. D., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., Tronrud, D. E., Ten Eyck, L. F., Lamzin, V. S., Perrakis, A., Wilson, K. S., Laskowski, R. A., MacArthur, M. W., Thornton, J. M., Kraulis, P. J., Richardson, D. C., Richardson, J. S., Kabsch, W. and Sheldrick, G. M. 2006. Programs and program systems in wide use. International Tables for Crystallography. F:25:25.2:695–743.

Author Information

  1. 1

    Biocrystallography Laboratory, VA Medical Center, PO Box 12055, University Drive C, Pittsburgh, PA 15240, USA, and Department of Pharmacology, University of Pittsburgh School of Medicine, 1340 BSTWR, Pittsburgh, PA 15261, USA

  2. 2

    Department of Chemistry, University of York, York YO1 5DD, England

  3. 3

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 90109, USA

  4. 4

    Department of Physics, University of York, York YO1 5DD, England

  5. 5

    Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory (SSRL), Stanford University, 1201 Welch Road, MSLS P210, Stanford, CA 94305, USA

  6. 6

    The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA

  7. 7

    Graduate Group in Biophysics, Box 0448, University of California, San Francisco, CA 94143, USA

  8. 8

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

  9. 9

    Protein Data Bank, Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA

  10. 10

    Department of Mathematical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2G1

  11. 11

    Department of Haematology, University of Cambridge, Wellcome Trust Centre for Molecular Mechanisms in Disease, CIMR, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England

  12. 12

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA

  13. 13

    Laboratoire de Biologie Structurale (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch (CU de Strasbourg), France

  14. 14

    Howard Hughes Medical Institute, Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403-1229, USA

  15. 15

    San Diego Supercomputer Center 0505, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA

  16. 16

    European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestr. 85, 22603 Hamburg, Germany

  17. 17

    European Molecular Biology Laboratory (EMBL), Grenoble Outstation, c/o ILL, Avenue des Martyrs, BP 156, 38042 Grenoble CEDEX 9, France

  18. 18

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England

  19. 19

    Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England

  20. 20

    Biochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England

  21. 21

    Biochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England, and Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England

  22. 22

    Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, SE-106 91 Stockholm, Sweden

  23. 23

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710-3711, USA

  24. 24

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany

  25. 25

    Lehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany

Publication History

  1. Published Online: 1 JAN 2006

Abstract

Macromolecular programs and program systems in wide use are described. The chapter covers PHASES; DM/DMMULTI, software for phase improvement by density modification; the structure-determination language of the Crystallography & NMR System; the TNT refinement package; the ARP/wARP suite for automated construction and refinement of protein models; validation of protein-structure coordinates with PROCHECK; MolScript; MAGE, PROBE and kinemages; XDS; and macromolecular applications of SHELX.

Keywords:

  • ARP/wARP;
  • CNS;
  • Crystallography & NMR System;
  • DM/DMMULTI;
  • MAGE;
  • MolScript;
  • PHASES;
  • PROBE;
  • PROCHECK;
  • Raster3D;
  • SHELX;
  • SHELXPRO;
  • TNT;
  • XDS;
  • animation;
  • anisotropic scaling;
  • approximate-likelihood method;
  • atomic displacement parameters;
  • conjugate-gradient method;
  • constraints;
  • data processing;
  • density modification;
  • direct methods;
  • disorder;
  • displaying structures;
  • electron-density averaging;
  • fast Fourier transform;
  • Fourier maps;
  • Fourier syntheses in PHASES;
  • Fourier transforms;
  • free-atom model;
  • heavy-atom location;
  • histogram matching;
  • hybrid models;
  • kinemages;
  • least-squares methods;
  • local scaling;
  • maximum likelihood;
  • model building;
  • model rebuilding;
  • molecular graphics;
  • molecular masks;
  • multiple-crystal-form averaging;
  • negative-density truncation in PHASES;
  • noncrystallographic symmetry;
  • OpenGL;
  • outliers;
  • Patterson functions;
  • Patterson maps;
  • phase combination;
  • phase extension;
  • phase improvement;
  • phase refinement;
  • phasing;
  • preconditioned conjugate-gradient method;
  • reciprocal-space refinement in ARP/wARP;
  • refinement;
  • relative Wilson scaling;
  • restraints;
  • rigid-group refinement;
  • scaling;
  • Sim weighting;
  • simulated annealing;
  • skeletonization;
  • solvent flattening;
  • solvent masks;
  • standard uncertainty;
  • structure determination;
  • structure representation;
  • structure validation;
  • structure-determination language;
  • target functions;
  • twinning;
  • Virtual Reality Modeling Language;
  • Wilson scaling