Molecular modelling and graphics

Diamond, R.

doi:10.1107/97809553602060000561

International Tables for Crystallography (2006). Vol. B. ch. 3.3, pp. 360-384 | 1 | 2 |
https://doi.org/10.1107/97809553602060000561

Chapter 3.3. Molecular modelling and graphics

3.3. Molecular modelling and graphics (pp. 360-384) | html | pdf | chapter contents |
R. Diamond
- 3.3.1. Graphics (pp. 360-376) | html | pdf |
  - 3.3.1.1. Coordinate systems, notation and standards (pp. 360-361) | html | pdf |
    - 3.3.1.1.1. Cartesian and crystallographic coordinates (p. 360) | html | pdf |
    - 3.3.1.1.2. Homogeneous coordinates (pp. 360-361) | html | pdf |
    - 3.3.1.1.3. Notation (p. 361) | html | pdf |
    - 3.3.1.1.4. Standards (p. 361) | html | pdf |
  - 3.3.1.2. Orthogonal (or rotation) matrices (pp. 361-367) | html | pdf |
    - 3.3.1.2.1. General form (pp. 361-363) | html | pdf |
    - 3.3.1.2.2. Measurement of rotations and strains from coordinates (pp. 364-366) | html | pdf |
    - 3.3.1.2.3. Orthogonalization of impure rotations (p. 367) | html | pdf |
    - 3.3.1.2.4. Eigenvalues and eigenvectors of orthogonal matrices (p. 367) | html | pdf |
  - 3.3.1.3. Projection transformations and spaces (pp. 367-373) | html | pdf |
    - 3.3.1.3.1. Definitions (pp. 367-368) | html | pdf |
    - 3.3.1.3.2. Translation (p. 368) | html | pdf |
    - 3.3.1.3.3. Rotation (p. 368) | html | pdf |
    - 3.3.1.3.4. Scale (p. 368) | html | pdf |
    - 3.3.1.3.5. Windowing and perspective (pp. 368-370) | html | pdf |
    - 3.3.1.3.6. Stereoviews (p. 370) | html | pdf |
    - 3.3.1.3.7. Viewports (pp. 370-371) | html | pdf |
    - 3.3.1.3.8. Compound transformations (pp. 371-372) | html | pdf |
    - 3.3.1.3.9. Inverse transformations (p. 372) | html | pdf |
    - 3.3.1.3.10. The three-axis joystick (pp. 372-373) | html | pdf |
    - 3.3.1.3.11. Other useful rotations (p. 373) | html | pdf |
    - 3.3.1.3.12. Symmetry (p. 373) | html | pdf |
  - 3.3.1.4. Modelling transformations (pp. 373-374) | html | pdf |
    - 3.3.1.4.1. Rotation about a bond (p. 373) | html | pdf |
    - 3.3.1.4.2. Stacked transformations (pp. 373-374) | html | pdf |
  - 3.3.1.5. Drawing techniques (pp. 374-376) | html | pdf |
    - 3.3.1.5.1. Types of hardware (pp. 374-375) | html | pdf |
    - 3.3.1.5.2. Optimization of line drawings (p. 375) | html | pdf |
    - 3.3.1.5.3. Representation of surfaces by lines (p. 375) | html | pdf |
    - 3.3.1.5.4. Representation of surfaces by dots (p. 375) | html | pdf |
    - 3.3.1.5.5. Representation of surfaces by shading (pp. 375-376) | html | pdf |
    - 3.3.1.5.6. Advanced hidden-line and hidden-surface algorithms (p. 376) | html | pdf |
- 3.3.2. Molecular modelling, problems and approaches (pp. 377-380) | html | pdf |
  - 3.3.2.1. Connectivity (p. 377) | html | pdf |
    - 3.3.2.1.1. Connectivity tables (p. 377) | html | pdf |
    - 3.3.2.1.2. Implied connectivity (p. 377) | html | pdf |
  - 3.3.2.2. Modelling methods (pp. 377-380) | html | pdf |
    - 3.3.2.2.1. Methods based on conformational variables (pp. 378-379) | html | pdf |
    - 3.3.2.2.2. Methods based on positional coordinates (p. 379) | html | pdf |
    - 3.3.2.2.3. Approaches to the problem of multiple minima (pp. 379-380) | html | pdf |
- 3.3.3. Implementations (pp. 380-384) | html | pdf |
  - 3.3.3.1. Systems for the display and modification of retrieved data (pp. 380-381) | html | pdf |
    - 3.3.3.1.1. ORTEP (p. 380) | html | pdf |
    - 3.3.3.1.2. Feldmann's system (pp. 380-381) | html | pdf |
    - 3.3.3.1.3. Lesk & Hardman software (p. 381) | html | pdf |
    - 3.3.3.1.4. GRAMPS (p. 381) | html | pdf |
    - 3.3.3.1.5. Takenaka & Sasada's system (p. 381) | html | pdf |
    - 3.3.3.1.6. MIDAS (p. 381) | html | pdf |
    - 3.3.3.1.7. Insight (p. 381) | html | pdf |
    - 3.3.3.1.8. PLUTO (p. 381) | html | pdf |
    - 3.3.3.1.9. MDKINO (p. 381) | html | pdf |
  - 3.3.3.2. Molecular-modelling systems based on electron density (pp. 381-384) | html | pdf |
    - 3.3.3.2.1. CHEMGRAF (pp. 381-382) | html | pdf |
    - 3.3.3.2.2. GRIP (p. 382) | html | pdf |
    - 3.3.3.2.3. Barry, Denson & North's systems (p. 382) | html | pdf |
    - 3.3.3.2.4. MMS-X (p. 382) | html | pdf |
    - 3.3.3.2.5. Texas A&M University system (p. 382) | html | pdf |
    - 3.3.3.2.6. Bilder (pp. 382-383) | html | pdf |
    - 3.3.3.2.7. Frodo (p. 383) | html | pdf |
    - 3.3.3.2.8. Guide (p. 383) | html | pdf |
    - 3.3.3.2.9. HYDRA (p. 383) | html | pdf |
    - 3.3.3.2.10. O (p. 384) | html | pdf |
  - 3.3.3.3. Molecular-modelling systems based on other criteria (p. 384) | html | pdf |
    - 3.3.3.3.1. Molbuild , Rings , PRXBLD and MM2/MMP2 (p. 384) | html | pdf |
    - 3.3.3.3.2. Script (p. 384) | html | pdf |
    - 3.3.3.3.3. CHARMM (p. 384) | html | pdf |
    - 3.3.3.3.4. Commercial systems (p. 384) | html | pdf |
- References | html | pdf |
- Figures
  - Fig. 3.3.1.1. The relationship between display-space coordinates (X, Y, Z, W) and picture-space coordinates (x, y, z, w) derived from them by the window transformation, U (p. 369) | html | pdf |
  - Fig. 3.3.1.2. Schematic representation of a simple branched-chain molecule with a stationary root and two extremities (p. 374) | html | pdf |

Chapter 3.3. Molecular modelling and graphics

Contents