Chapter

Chapter 3.3 Molecular modelling and graphics

Reciprocal space

Second Online Edition (2010)

Part 3. Dual bases in crystallographic computing

  1. R. Diamond1,
  2. L. M. D. Cranswick2

Published Online: 1 JUN 2010

DOI: 10.1107/97809553602060000770

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Diamond, R. and Cranswick, L. M. D. 2010. Molecular modelling and graphics. International Tables for Crystallography. B:3:3.3:418–448.

Author Information

  1. 1

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England

  2. 2

    Neutron Program for Materials Research, National Research Council Canada, Building 459, Chalk River Laboratories, Chalk River, Ontario, Canada K0J 1J0

Publication History

  1. Published Online: 1 JUN 2010

Abstract

This chapter is in four parts, the first three being written by R. Diamond and the fourth by L. M. D. Cranswick. The first of these (Section 3.3.1) addresses many aspects of computer graphics relevant to both vector and raster machines and includes a discussion of coordinate transformations, including some of the many forms of orthogonal transformations that may arise, superpositions, projective geometry using homogeneous coordinates, perspective and stereo, and the reverse transformations involved in identifying positions in data space from positions on the screen. It also considers transformations affecting drawing which result from changes to molecular features, such as rotations about single bonds, and the organization of such transformations in stacks. This part concludes with a discussion of various drawing techniques as they relate to both vector and raster devices. The second part (Section 3.3.2) is concerned with molecular modelling and reviews methods of specifying connectivity within molecules. It also compares modelling methods for which the atomic coordinates are treated as independent variables with those for which other conformational variables are treated as independent and, for the latter, a solution to the problems arising from chain continuity in polymers, or from the closure of flexible rings, is given. The third part (Section 3.3.3) gives outline descriptions of some 22 software systems developed in crystallography, most of them intended mainly for macromolecular work. This collection is now of mainly historical interest. It was updated for the second edition of this volume but it has not been altered further for the third edition. The fourth part (Section 3.3.4), which has been written for the third edition, brings up to date the list of available software with 32 new entries drawn from small-molecule and inorganic crystallography, including topological analysis and the presentation of magnetic and incommensurate structures.

Keywords:

  • molecular modelling;
  • graphics;
  • coordinates;
  • orthogonal matrices;
  • transformations;
  • rotations;
  • rotation matrices;
  • translations;
  • windowing;
  • perspective;
  • scale;
  • stereoviews;
  • viewports;
  • compound transformations;
  • stacked transformations;
  • line drawings;
  • representation of surfaces;
  • hidden-line algorithms;
  • hidden-surface algorithms;
  • symmetry;
  • connectivity;
  • surfaces;
  • implied connectivity;
  • ATOMS;
  • Balls&Sticks;
  • BALSAC;
  • Bilder;
  • Cameron;
  • CaRIne;
  • Crystallographica;
  • CrystalMaker;
  • Crystal Studio;
  • CrystMol;
  • CHARMM;
  • CHEMGRAF;
  • Diamond;
  • DrawXTL;
  • FpStudio;
  • Frodo;
  • GRAMPS;
  • GRETEP;
  • GRIP;
  • Guide;
  • HYDRA;
  • Insight;
  • MDKINO;
  • Mercury;
  • MIDAS;
  • MM2/MMP2;
  • MMS-X;
  • Molbuild;
  • MolXtl;
  • O;
  • OLEX;
  • ORTEP;
  • ORTEP-III;
  • ORTEP-3 for Windows;
  • ORTEX;
  • Oscail X;
  • PEANUT;
  • Platon;
  • PLUTO;
  • Pluton;
  • PowderCell;
  • PRJMS;
  • PRXBLD;
  • Rings;
  • SCHAKAL;
  • Script;
  • STRUPLO;
  • STRUPLO for Windows;
  • STRUVIR;
  • VENUS;
  • XmLmctep;
  • X-Seed;
  • Xtal-3D;
  • XtalDraw