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

Chapter 3.3. Molecular modelling and graphics

Contents

  • 3.3. Molecular modelling and graphics  (pp. 360-384) | html | pdf | chapter contents |
    • 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 |