International Tables for Crystallography (2010). Vol. B, ch. 3.3, pp. 418-448   | 1 | 2 |
doi: 10.1107/97809553602060000770

Chapter 3.3. Molecular modelling and graphics

Contents

  • 3.3. Molecular modelling and graphics  (pp. 418-448) | html | pdf | chapter contents |
    • 3.3.1. Graphics  (pp. 418-434) | html | pdf |
      • 3.3.1.1. Coordinate systems, notation and standards  (pp. 418-419) | html | pdf |
        • 3.3.1.1.1. Cartesian and crystallographic coordinates  (p. 418) | html | pdf |
        • 3.3.1.1.2. Homogeneous coordinates  (pp. 418-419) | html | pdf |
        • 3.3.1.1.3. Notation  (p. 419) | html | pdf |
        • 3.3.1.1.4. Standards  (p. 419) | html | pdf |
      • 3.3.1.2. Orthogonal (or rotation) matrices  (pp. 419-426) | html | pdf |
        • 3.3.1.2.1. General form  (pp. 419-422) | html | pdf |
        • 3.3.1.2.2. Measurement of rotations and strains from coordinates  (pp. 422-425) | html | pdf |
        • 3.3.1.2.3. Orthogonalization of impure rotations  (p. 425) | html | pdf |
        • 3.3.1.2.4. Eigenvalues and eigenvectors of orthogonal matrices  (pp. 425-426) | html | pdf |
      • 3.3.1.3. Projection transformations and spaces  (pp. 426-431) | html | pdf |
        • 3.3.1.3.1. Definitions  (p. 426) | html | pdf |
        • 3.3.1.3.2. Translation  (p. 426) | html | pdf |
        • 3.3.1.3.3. Rotation  (p. 426) | html | pdf |
        • 3.3.1.3.4. Scale  (p. 426) | html | pdf |
        • 3.3.1.3.5. Windowing and perspective  (pp. 426-428) | html | pdf |
        • 3.3.1.3.6. Stereoviews  (p. 428) | html | pdf |
        • 3.3.1.3.7. Viewports  (pp. 428-429) | html | pdf |
        • 3.3.1.3.8. Compound transformations  (pp. 429-430) | html | pdf |
        • 3.3.1.3.9. Inverse transformations  (p. 430) | html | pdf |
        • 3.3.1.3.10. The three-axis joystick  (pp. 430-431) | html | pdf |
        • 3.3.1.3.11. Other useful rotations  (p. 431) | html | pdf |
        • 3.3.1.3.12. Symmetry  (p. 431) | html | pdf |
      • 3.3.1.4. Modelling transformations  (pp. 431-432) | html | pdf |
        • 3.3.1.4.1. Rotation about a bond  (p. 431) | html | pdf |
        • 3.3.1.4.2. Stacked transformations  (pp. 431-432) | html | pdf |
      • 3.3.1.5. Drawing techniques  (pp. 432-434) | html | pdf |
        • 3.3.1.5.1. Types of hardware  (pp. 432-433) | html | pdf |
        • 3.3.1.5.2. Optimization of line drawings  (p. 433) | html | pdf |
        • 3.3.1.5.3. Representation of surfaces by lines  (p. 433) | html | pdf |
        • 3.3.1.5.4. Representation of surfaces by dots  (p. 433) | html | pdf |
        • 3.3.1.5.5. Representation of surfaces by shading  (pp. 433-434) | html | pdf |
        • 3.3.1.5.6. Advanced hidden-line and hidden-surface algorithms  (p. 434) | html | pdf |
    • 3.3.2. Molecular modelling, problems and approaches  (pp. 434-438) | html | pdf |
      • 3.3.2.1. Connectivity  (p. 435) | html | pdf |
        • 3.3.2.1.1. Connectivity tables  (p. 435) | html | pdf |
        • 3.3.2.1.2. Implied connectivity  (p. 435) | html | pdf |
      • 3.3.2.2. Modelling methods  (pp. 435-438) | html | pdf |
        • 3.3.2.2.1. Methods based on conformational variables  (pp. 435-437) | html | pdf |
        • 3.3.2.2.2. Methods based on positional coordinates  (p. 437) | html | pdf |
        • 3.3.2.2.3. Approaches to the problem of multiple minima  (pp. 437-438) | html | pdf |
    • 3.3.3. Implementations  (pp. 438-442) | html | pdf |
      • 3.3.3.1. Systems for the display and modification of retrieved data  (pp. 438-439) | html | pdf |
        • 3.3.3.1.1. ORTEP   (p. 438) | html | pdf |
        • 3.3.3.1.2. Feldmann's system  (pp. 438-439) | html | pdf |
        • 3.3.3.1.3. Lesk & Hardman software  (p. 439) | html | pdf |
        • 3.3.3.1.4. GRAMPS   (p. 439) | html | pdf |
        • 3.3.3.1.5. Takenaka & Sasada's system  (p. 439) | html | pdf |
        • 3.3.3.1.6. MIDAS   (p. 439) | html | pdf |
        • 3.3.3.1.7. Insight   (p. 439) | html | pdf |
        • 3.3.3.1.8. PLUTO   (p. 439) | html | pdf |
        • 3.3.3.1.9. MDKINO   (p. 439) | html | pdf |
      • 3.3.3.2. Molecular-modelling systems based on electron density  (pp. 439-442) | html | pdf |
        • 3.3.3.2.1. CHEMGRAF   (pp. 439-440) | html | pdf |
        • 3.3.3.2.2. GRIP   (p. 440) | html | pdf |
        • 3.3.3.2.3. Barry, Denson & North's systems  (p. 440) | html | pdf |
        • 3.3.3.2.4. MMS-X   (p. 440) | html | pdf |
        • 3.3.3.2.5. Texas A&M University system  (p. 440) | html | pdf |
        • 3.3.3.2.6. Bilder   (pp. 440-441) | html | pdf |
        • 3.3.3.2.7. Frodo   (p. 441) | html | pdf |
        • 3.3.3.2.8. Guide   (p. 441) | html | pdf |
        • 3.3.3.2.9. HYDRA   (p. 441) | html | pdf |
        • 3.3.3.2.10. O   (pp. 441-442) | html | pdf |
      • 3.3.3.3. Molecular-modelling systems based on other criteria  (p. 442) | html | pdf |
        • 3.3.3.3.1. Molbuild , Rings , PRXBLD and MM2/MMP2   (p. 442) | html | pdf |
        • 3.3.3.3.2. Script   (p. 442) | html | pdf |
        • 3.3.3.3.3. CHARMM   (p. 442) | html | pdf |
        • 3.3.3.3.4. Commercial systems  (p. 442) | html | pdf |
    • 3.3.4. Graphics software for the display of small and medium-sized molecules  (pp. 442-445) | html | pdf |
      • 3.3.4.1. Introduction  (pp. 442-443) | html | pdf |
      • 3.3.4.2. Types of crystal structure display and functionality  (pp. 443-445) | html | pdf |
        • 3.3.4.2.1. Ball and stick  (p. 443) | html | pdf |
        • 3.3.4.2.2. Anisotropic displacement parameters  (p. 443) | html | pdf |
        • 3.3.4.2.3. Mean-square displacement amplitude  (p. 443) | html | pdf |
        • 3.3.4.2.4. Polyhedral display  (pp. 443-444) | html | pdf |
        • 3.3.4.2.5. Cartesian coordinates  (p. 445) | html | pdf |
        • 3.3.4.2.6. Comparing or overlaying crystal structures  (p. 445) | html | pdf |
        • 3.3.4.2.7. Extended structures and topology analysis  (p. 445) | html | pdf |
        • 3.3.4.2.8. Magnetic crystal structure display  (p. 445) | html | pdf |
        • 3.3.4.2.9. Incommensurate crystal structures  (p. 445) | 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. 427) | html | pdf |
      • Fig. 3.3.1.2. Schematic representation of a simple branched-chain molecule with a stationary root and two extremities  (p. 432) | html | pdf |
    • Tables
      • Table 3.3.4.1. Functionality of software for crystal structure display  (p. 443) | html | pdf |
      • Table 3.3.4.2. Availability of software for crystal structure display  (p. 444) | html | pdf |