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 |
- 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 |
- 25.2.1.3. Merging and scaling native and derivative data (pp. 696-697) | html | pdf |
- 25.2.1.4. Fourier-map calculations (p. 697) | html | pdf |
- 25.2.1.5. Structure-factor and phase calculations (pp. 697-698) | html | pdf |
- 25.2.1.6. Parameter refinement (pp. 698-699) | html | pdf |
- 25.2.1.7. Origin and hand correlation, and completing the heavy-atom substructure (pp. 699-700) | html | pdf |
- 25.2.1.8. Solvent flattening and negative-density truncation (pp. 700-701) | html | pdf |
- 25.2.1.9. Phase combination and extension procedures (pp. 701-702) | 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 |
- 25.2.1.10.3. Averaging mask construction (p. 703) | html | pdf |
- 25.2.1.10.4. Map 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 |
- 25.2.1.12. Graphical capabilities (pp. 704-705) | 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 |
- 25.2.1.1. Overall scope of the package (pp. 695-696) | 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 |
- 25.2.2.5. 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 |
- 25.2.4.4. 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 |
- 25.2.5.1. Refinement and model building are two sides of modelling a structure (pp. 720-721) | 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 |
- 25.2.8. 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 |
- 25.2.10. 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 |
- 25.2.10.4. 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
- 25.2.1. PHASES (pp. 695-705) | html | pdf |