International Tables for Crystallography (2006). Vol. F. ch. 25.2, pp. 695-743
https://doi.org/10.1107/97809553602060000724

Chapter 25.2. Programs and program systems in wide use

Contents

  • 25.2. Programs and program systems in wide use  (pp. 695-743) | html | pdf | chapter contents |
    W. Furey, K. D. Cowtan, K. Y. J. Zhang, P. Main, A. T. Brunger, P. D. Adams, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, D. E. Tronrud, L. F. Ten Eyck, V. S. Lamzin, A. Perrakis, K. S. Wilson, R. A. Laskowski, M. W. MacArthur, J. M. Thornton, P. J. Kraulis, D. C. Richardson, J. S. Richardson, W. Kabsch and G. M. Sheldrick
    • 25.2.1. PHASES  (pp. 695-705) | html | pdf |
      W. Furey
      • 25.2.1.1. Overall scope of the package  (pp. 695-696) | html | pdf |
        • 25.2.1.1.1. Isomorphous replacement, anomalous scattering and MAD phasing  (p. 695) | html | pdf |
        • 25.2.1.1.2. Solvent flattening and negative-density truncation  (p. 695) | html | pdf |
        • 25.2.1.1.3. Noncrystallographic symmetry averaging  (p. 695) | html | pdf |
        • 25.2.1.1.4. Partial structure phase combination and phase extension  (p. 696) | html | pdf |
      • 25.2.1.2. Design principles  (p. 696) | html | pdf |
        • 25.2.1.2.1. General program structure and data flow  (p. 696) | html | pdf |
        • 25.2.1.2.2. Parameter and cumulative log files  (p. 696) | html | pdf |
      • 25.2.1.3. Merging and scaling native and derivative data  (pp. 696-697) | html | pdf |
        • 25.2.1.3.1. Relative Wilson scaling  (p. 696) | html | pdf |
        • 25.2.1.3.2. Global anisotropic scaling  (p. 697) | html | pdf |
        • 25.2.1.3.3. Local scaling  (p. 697) | html | pdf |
        • 25.2.1.3.4. Outlier rejection  (p. 697) | html | pdf |
      • 25.2.1.4. Fourier-map calculations  (p. 697) | html | pdf |
        • 25.2.1.4.1. Submaps  (p. 697) | html | pdf |
        • 25.2.1.4.2. Orthogonal and skewed maps  (p. 697) | html | pdf |
        • 25.2.1.4.3. Graphics maps and skeletonization  (p. 697) | html | pdf |
        • 25.2.1.4.4. Peak search  (p. 697) | html | pdf |
      • 25.2.1.5. Structure-factor and phase calculations  (pp. 697-698) | html | pdf |
        • 25.2.1.5.1. By heavy-atom or anomalous-scattering methods  (pp. 697-698) | html | pdf |
        • 25.2.1.5.2. Directly from atomic coordinates  (p. 698) | html | pdf |
        • 25.2.1.5.3. By map inversion  (p. 698) | html | pdf |
      • 25.2.1.6. Parameter refinement  (pp. 698-699) | html | pdf |
        • 25.2.1.6.1. Against amplitude differences  (p. 698) | html | pdf |
        • 25.2.1.6.2. By minimizing lack of closure  (pp. 698-699) | html | pdf |
          • 25.2.1.6.2.1. `Classical' phase refinement  (p. 699) | html | pdf |
          • 25.2.1.6.2.2. Approximate-likelihood method  (p. 699) | html | pdf |
          • 25.2.1.6.2.3. Using external phase information  (p. 699) | html | pdf |
        • 25.2.1.6.3. Rigid-group refinement  (p. 699) | html | pdf |
      • 25.2.1.7. Origin and hand correlation, and completing the heavy-atom substructure  (pp. 699-700) | html | pdf |
        • 25.2.1.7.1. Difference and cross-difference Fourier syntheses  (pp. 699-700) | html | pdf |
        • 25.2.1.7.2. Bijvoet difference and cross-Bijvoet difference Fourier syntheses  (p. 700) | html | pdf |
      • 25.2.1.8. Solvent flattening and negative-density truncation  (pp. 700-701) | html | pdf |
        • 25.2.1.8.1. Mask construction  (pp. 700-701) | html | pdf |
          • 25.2.1.8.1.1. Automated mask construction  (pp. 700-701) | html | pdf |
          • 25.2.1.8.1.2. Masks from atomic coordinates  (p. 701) | html | pdf |
          • 25.2.1.8.1.3. Mask verification and manual editing  (p. 701) | html | pdf |
        • 25.2.1.8.2. The flattening and truncation procedure  (p. 701) | html | pdf |
      • 25.2.1.9. Phase combination and extension procedures  (pp. 701-702) | html | pdf |
        • 25.2.1.9.1. Modified Sim weights  (p. 701) | html | pdf |
        • 25.2.1.9.2. σA weights  (p. 702) | html | pdf |
        • 25.2.1.9.3. Damping contributions  (p. 702) | html | pdf |
        • 25.2.1.9.4. Phase extension  (p. 702) | html | pdf |
      • 25.2.1.10. Noncrystallographic symmetry calculations  (pp. 702-704) | html | pdf |
        • 25.2.1.10.1. Operator representation and definitions  (p. 702) | html | pdf |
        • 25.2.1.10.2. Operator refinement  (pp. 702-703) | html | pdf |
          • 25.2.1.10.2.1. Simple rotational symmetry  (p. 703) | html | pdf |
          • 25.2.1.10.2.2. Complex rotational and/or translational symmetry  (p. 703) | html | pdf |
        • 25.2.1.10.3. Averaging mask construction  (p. 703) | html | pdf |
        • 25.2.1.10.4. Map averaging  (p. 703) | html | pdf |
          • 25.2.1.10.4.1. Single-crystal averaging  (p. 703) | html | pdf |
          • 25.2.1.10.4.2. Multiple-crystal averaging  (p. 703) | html | pdf |
        • 25.2.1.10.5. Phase combination and extension  (pp. 703-704) | html | pdf |
      • 25.2.1.11. Automated iterative processing  (p. 704) | html | pdf |
        • 25.2.1.11.1. The DOALL procedure  (p. 704) | html | pdf |
        • 25.2.1.11.2. The EXTNDAVG and EXTNDAVG_MC procedures  (p. 704) | html | pdf |
      • 25.2.1.12. Graphical capabilities  (pp. 704-705) | html | pdf |
        • 25.2.1.12.1. Pseudo-precession photographs  (p. 704) | html | pdf |
        • 25.2.1.12.2. Interactive contouring or mask editing  (p. 704) | html | pdf |
        • 25.2.1.12.3. Off-line contouring  (p. 704) | html | pdf |
        • 25.2.1.12.4. Generic plot files and drivers  (p. 705) | html | pdf |
          • 25.2.1.12.4.1. GL displays  (p. 705) | html | pdf |
          • 25.2.1.12.4.2. X-Window displays  (p. 705) | html | pdf |
          • 25.2.1.12.4.3. PostScript files  (p. 705) | html | pdf |
          • 25.2.1.12.4.4. Tektronix output  (p. 705) | html | pdf |
      • 25.2.1.13. Auxiliary programs  (p. 705) | html | pdf |
        • 25.2.1.13.1. Coordinate conversions  (p. 705) | html | pdf |
        • 25.2.1.13.2. NC symmetry operator conversions  (p. 705) | html | pdf |
        • 25.2.1.13.3. Binary or formatted file conversions  (p. 705) | html | pdf |
        • 25.2.1.13.4. Importing phase information  (p. 705) | html | pdf |
        • 25.2.1.13.5. Phase set comparisons  (p. 705) | html | pdf |
    • 25.2.2. DM/DMMULTI software for phase improvement by density modification  (pp. 705-710) | html | pdf |
      K. D. Cowtan, K. Y. J. Zhang and P. Main
      • 25.2.2.1. Introduction  (pp. 705-706) | html | pdf |
      • 25.2.2.2. Program operation  (p. 706) | html | pdf |
      • 25.2.2.3. Preparation of input data  (p. 706) | html | pdf |
      • 25.2.2.4. Choice of modes  (pp. 706-709) | html | pdf |
        • 25.2.2.4.1. Density-modification modes  (p. 707) | html | pdf |
        • 25.2.2.4.2. Phase-combination modes  (pp. 707-708) | html | pdf |
        • 25.2.2.4.3. Phase-extension schemes  (pp. 708-709) | html | pdf |
      • 25.2.2.5. Code description  (pp. 709-710) | html | pdf |
        • 25.2.2.5.1. Scaling  (p. 709) | html | pdf |
        • 25.2.2.5.2. Solvent-mask determination  (pp. 709-710) | html | pdf |
        • 25.2.2.5.3. Averaging-mask determination  (p. 710) | html | pdf |
        • 25.2.2.5.4. Fourier transforms  (p. 710) | html | pdf |
        • 25.2.2.5.5. Histogram matching  (p. 710) | html | pdf |
        • 25.2.2.5.6. Averaging  (p. 710) | html | pdf |
        • 25.2.2.5.7. Multi-crystal averaging  (p. 710) | html | pdf |
    • 25.2.3. The structure-determination language of the Crystallography & NMR System  (pp. 710-716) | html | pdf |
      A. T. Brunger, P. D. Adams, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, N. S. Pannu, R. J. Read, L. M. Rice and T. Simonson
      • 25.2.3.1. Introduction  (p. 710) | html | pdf |
      • 25.2.3.2. The CNS language  (pp. 711-712) | html | pdf |
      • 25.2.3.3. Symbols and parameters  (p. 712) | html | pdf |
      • 25.2.3.4. Statistical functions  (p. 712) | html | pdf |
      • 25.2.3.5. Symbolic target function  (pp. 712-713) | html | pdf |
      • 25.2.3.6. Modules and procedures  (p. 714) | html | pdf |
      • 25.2.3.7. Task files  (p. 715) | html | pdf |
      • 25.2.3.8. HTML interface  (p. 715) | html | pdf |
      • 25.2.3.9. Example: combined maximum-likelihood and simulated-annealing refinement  (pp. 715-716) | html | pdf |
      • 25.2.3.10. Conclusions  (p. 716) | html | pdf |
    • 25.2.4. The TNT refinement package  (pp. 716-720) | html | pdf |
      D. E. Tronrud and L. F. Ten Eyck
      • 25.2.4.1. Scope and function of the package  (pp. 716-717) | html | pdf |
      • 25.2.4.2. Historical context  (p. 717) | html | pdf |
      • 25.2.4.3. Design principles  (pp. 717-718) | html | pdf |
        • 25.2.4.3.1. Refinement should be simple to run  (p. 717) | html | pdf |
        • 25.2.4.3.2. Refinement should run quickly and use as little memory as possible  (pp. 717-718) | html | pdf |
        • 25.2.4.3.3. The source code should not require customization for each project  (p. 718) | html | pdf |
      • 25.2.4.4. Current structure of the package  (p. 718) | html | pdf |
      • 25.2.4.5. Innovations first introduced in TNT  (pp. 718-719) | html | pdf |
        • 25.2.4.5.1. Identifying and restraining symmetry-related contacts (1982)  (p. 719) | html | pdf |
        • 25.2.4.5.2. The ability of a single package to perform both individual atom and rigid-body refinement (1982)  (p. 719) | html | pdf |
        • 25.2.4.5.3. Space-group optimized FFTs for all space groups (1989)  (p. 719) | html | pdf |
        • 25.2.4.5.4. Modelling bulk solvent scattering via local scaling (∼1989)  (p. 719) | html | pdf |
        • 25.2.4.5.5. Preconditioned conjugate-gradient minimization (1990)  (p. 719) | html | pdf |
        • 25.2.4.5.6. Restraining stereochemistry of chemical links to symmetry-related molecules (∼1992)  (p. 719) | html | pdf |
        • 25.2.4.5.7. Knowledge-based B-factor restraints (∼1994)  (p. 719) | html | pdf |
        • 25.2.4.5.8. Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998)  (p. 719) | html | pdf |
        • 25.2.4.5.9. Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998)  (p. 719) | html | pdf |
      • 25.2.4.6. TNT as a research tool  (pp. 719-720) | html | pdf |
        • 25.2.4.6.1. Michael Chapman's real-space refinement package  (p. 719) | html | pdf |
        • 25.2.4.6.2. Gerard Bricogne's Buster refinement package  (p. 719) | html | pdf |
        • 25.2.4.6.3. Randy Read's maximum-likelihood function  (p. 720) | html | pdf |
        • 25.2.4.6.4. J. P. Abrahams' likelihood-weighted noncrystallographic symmetry restraints  (p. 720) | html | pdf |
    • 25.2.5. The ARP/wARP suite for automated construction and refinement of protein models  (pp. 720-722) | html | pdf |
      V. S. Lamzin, A. Perrakis and K. S. Wilson
      • 25.2.5.1. Refinement and model building are two sides of modelling a structure  (pp. 720-721) | html | pdf |
        • 25.2.5.1.1. Model update  (p. 720) | html | pdf |
        • 25.2.5.1.2. Model reconstruction  (pp. 720-721) | html | pdf |
        • 25.2.5.1.3. Representation of a map by free-atom models  (p. 721) | html | pdf |
        • 25.2.5.1.4. Hybrid models  (p. 721) | html | pdf |
        • 25.2.5.1.5. Real-space manipulation coupled with reciprocal-space refinement  (p. 721) | html | pdf |
      • 25.2.5.2. ARP/wARP applications  (pp. 721-722) | html | pdf |
        • 25.2.5.2.1. Model building from initial phases  (p. 721) | html | pdf |
        • 25.2.5.2.2. Refinement of molecular-replacement solutions  (p. 721) | html | pdf |
        • 25.2.5.2.3. Density modification via averaging of multiple refinements  (pp. 721-722) | html | pdf |
        • 25.2.5.2.4. Ab initio solution of metalloproteins  (p. 722) | html | pdf |
        • 25.2.5.2.5. Solvent building  (p. 722) | html | pdf |
      • 25.2.5.3. Applicability and requirements  (p. 722) | html | pdf |
      • 25.2.5.4. An example  (p. 722) | html | pdf |
    • 25.2.6. PROCHECK: validation of protein-structure coordinates  (pp. 722-725) | html | pdf |
      R. A. Laskowski, M. W. MacArthur and J. M. Thornton
      • 25.2.6.1. Introduction  (pp. 722-723) | html | pdf |
      • 25.2.6.2. The program   (p. 723) | html | pdf |
      • 25.2.6.3. The parameters  (p. 723) | html | pdf |
      • 25.2.6.4. Which parameters are best?  (pp. 723-724) | html | pdf |
      • 25.2.6.5. Input  (pp. 724-725) | html | pdf |
      • 25.2.6.6. Output produced  (p. 725) | html | pdf |
      • 25.2.6.7. Other validation tools  (p. 725) | html | pdf |
    • 25.2.7. MolScript  (pp. 725-727) | html | pdf |
      P. J. Kraulis
      • 25.2.7.1. Introduction  (p. 725) | html | pdf |
      • 25.2.7.2. Input  (p. 725) | html | pdf |
      • 25.2.7.3. Graphics  (pp. 725-726) | html | pdf |
        • 25.2.7.3.1. The coordinate system  (p. 725) | html | pdf |
        • 25.2.7.3.2. The graphics state  (pp. 725-726) | html | pdf |
        • 25.2.7.3.3. Graphics commands  (p. 726) | html | pdf |
        • 25.2.7.3.4. Atom and residue selection  (p. 726) | html | pdf |
        • 25.2.7.3.5. External objects  (p. 726) | html | pdf |
      • 25.2.7.4. Output  (p. 726) | html | pdf |
        • 25.2.7.4.1. PostScript  (p. 726) | html | pdf |
        • 25.2.7.4.2. Raster3D  (p. 726) | html | pdf |
        • 25.2.7.4.3. VRML97  (p. 726) | html | pdf |
        • 25.2.7.4.4. OpenGL  (p. 726) | html | pdf |
        • 25.2.7.4.5. Image files  (p. 726) | html | pdf |
      • 25.2.7.5. Utilities  (pp. 726-727) | html | pdf |
    • 25.2.8. MAGE, PROBE and kinemages  (pp. 727-730) | html | pdf |
      D. C. Richardson and J. S. Richardson
      • 25.2.8.1. Introduction to aims and concepts  (p. 727) | html | pdf |
      • 25.2.8.2. Use as a reader of existing kinemages  (p. 727) | html | pdf |
      • 25.2.8.3. Use for teaching  (pp. 727-728) | html | pdf |
      • 25.2.8.4. Use for research  (pp. 728-729) | html | pdf |
      • 25.2.8.5. Contact dots in crystallographic rebuilding  (p. 729) | html | pdf |
      • 25.2.8.6. Making kinemages  (pp. 729-730) | html | pdf |
      • 25.2.8.7. Software notes  (p. 730) | html | pdf |
    • 25.2.9. XDS  (pp. 730-734) | html | pdf |
      W. Kabsch
      • 25.2.9.1. Functional specification  (p. 730) | html | pdf |
      • 25.2.9.2. Components of the package  (pp. 730-734) | html | pdf |
        • 25.2.9.2.1. XDS  (pp. 730-733) | html | pdf |
        • 25.2.9.2.2. XPLAN  (p. 733) | html | pdf |
        • 25.2.9.2.3. XSCALE  (pp. 733-734) | html | pdf |
        • 25.2.9.2.4. VIEW  (p. 734) | html | pdf |
        • 25.2.9.2.5. XDSCONV  (p. 734) | html | pdf |
      • 25.2.9.3. Remarks  (p. 734) | html | pdf |
    • 25.2.10. Macromolecular applications of SHELX  (pp. 734-738) | html | pdf |
      G. M. Sheldrick
      • 25.2.10.1. Historical introduction to SHELX  (p. 734) | html | pdf |
      • 25.2.10.2. Program organization and philosophy  (p. 735) | html | pdf |
      • 25.2.10.3. Heavy-atom location using SHELXS and SHELXD  (pp. 735-736) | html | pdf |
        • 25.2.10.3.1. The Patterson map interpretation algorithm in SHELXS  (p. 735) | html | pdf |
        • 25.2.10.3.2. Integrated Patterson and direct methods: SHELXD  (p. 735) | html | pdf |
        • 25.2.10.3.3. Practical considerations  (p. 736) | html | pdf |
      • 25.2.10.4. Macromolecular refinement using SHELXL  (pp. 736-737) | html | pdf |
        • 25.2.10.4.1. Constraints and restraints  (p. 736) | html | pdf |
        • 25.2.10.4.2. Least-squares refinement algebra  (p. 736) | html | pdf |
        • 25.2.10.4.3. Full-matrix estimates of standard uncertainties  (p. 736) | html | pdf |
        • 25.2.10.4.4. Refinement of anisotropic displacement parameters  (pp. 736-737) | html | pdf |
        • 25.2.10.4.5. Similar geometry and NCS restraints  (p. 737) | html | pdf |
        • 25.2.10.4.6. Modelling disorder and solvent  (p. 737) | html | pdf |
        • 25.2.10.4.7. Twinned crystals  (p. 737) | html | pdf |
        • 25.2.10.4.8. The radius of convergence  (p. 737) | html | pdf |
      • 25.2.10.5. SHELXPRO – protein interface to SHELX  (pp. 737-738) | html | pdf |
      • 25.2.10.6. Distribution and support of SHELX  (p. 738) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 25.2.1.1. Flow chart for the major phasing path  (p. 696) | html | pdf |
      • Fig. 25.2.1.2. Relationships between noncrystallographic symmetry rotation axis direction, orthogonal reference system axes X, Y, Z and crystallographic axes  (p. 702) | html | pdf |
      • Fig. 25.2.2.1. (a) Input and output data for a DM calculation with no averaging  (p. 707) | html | pdf |
      • Fig. 25.2.2.2. (a) Flow chart for a simple DM calculation with free-Sim phase combination  (p. 708) | html | pdf |
      • Fig. 25.2.2.3. (a) Conceptual flowchart for a DMMULTI multi-crystal calculation  (p. 709) | html | pdf |
      • Fig. 25.2.3.1. CNS consists of five layers which are under user control  (p. 711) | html | pdf |
      • Fig. 25.2.3.2. Examples of compound symbols and compound parameters  (p. 712) | html | pdf |
      • Fig. 25.2.3.3. Example for statistical operations provided by the CNS language  (p. 712) | html | pdf |
      • Fig. 25.2.3.4. Examples of symbolic definition of a refinement target function and its derivatives with respect to the calculated structure-factor arrays  (p. 713) | html | pdf |
      • Fig. 25.2.3.5. Use of compound parameters within a module  (p. 713) | html | pdf |
      • Fig. 25.2.3.6. Example of (a) a CNS module and (b) the corresponding module invocation  (p. 714) | html | pdf |
      • Fig. 25.2.3.7. Procedures and features available in CNS for structure determination by X-ray crystallography  (p. 714) | html | pdf |
      • Fig. 25.2.3.8. Example of a typical CNS task file  (p. 715) | html | pdf |
      • Fig. 25.2.3.9. Example of a CNS HTML form page  (p. 715) | html | pdf |
      • Fig. 25.2.3.10. Use of the CNS HTML form page interface, emphasizing the correspondence between input fields in the form page and parameters in the task file  (p. 716) | html | pdf |
      • Fig. 25.2.5.1. A flow chart of the Automated Refinement Procedure  (p. 720) | html | pdf |
      • Fig. 25.2.6.1. PROCHECK Ramachandran plots  (p. 723) | html | pdf |
      • Fig. 25.2.6.2. Two of the residue-property plots generated by PROCHECK  (p. 724) | html | pdf |
      • Fig. 25.2.6.3. Schematic plots of various residue-by-residue properties  (p. 724) | html | pdf |
      • Fig. 25.2.8.1. A typical macromolecular kinemage  (p. 728) | html | pdf |
      • Fig. 25.2.8.2. A ribbon-schematic kinemage of ribonuclease A  (p. 728) | html | pdf |
      • Fig. 25.2.8.3. A thin slice through an all-atom contact kinemage showing the van der Waals interactions of Pro203 and neighbouring atoms in Zn elastase  (p. 728) | html | pdf |
      • Fig. 25.2.8.4. All-atom contact dots being used in O for model rebuilding during refinement of a Trp tRNA synthetase  (p. 729) | html | pdf |
    • Tables
      • Table 25.2.6.1. Summary of expected values for stereochemical parameters in well resolved structures  (p. 723) | html | pdf |
      • Table 25.2.9.1. Information exchange between program steps of XDS  (p. 731) | html | pdf |