International Tables for Crystallography (2006). Vol. F, ch. 25.2, pp. 695-743
doi: 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 |
    • 25.2.1. PHASES   (pp. 695-705) | html | pdf |
      • 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. σ A 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 |
      • 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 |
      • 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 |
      • 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 |
      • 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 |
      • 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 |
      • 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. Raster 3 D   (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 |
      • 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 |
      • 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 |
      • 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 |