Chapter

Chapter 3.3 Molecular modelling and graphics

Reciprocal space

First Online Edition (2006)

Part 3. Dual bases in crystallographic computing

  1. R. Diamond

Published Online: 1 JAN 2006

DOI: 10.1107/97809553602060000561

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Diamond, R. 2006. Molecular modelling and graphics. International Tables for Crystallography. B:3:3.3:360–384.

Author Information

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

Publication History

  1. Published Online: 1 JAN 2006

Abstract

This chapter is in three parts. 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 section 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, but was updated for the second edition.

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;
  • Bilder;
  • CHARMM;
  • CHEMGRAF;
  • Frodo;
  • GRAMPS;
  • GRIP;
  • Guide;
  • HYDRA;
  • Insight;
  • MDKINO;
  • MIDAS;
  • MM2/MMP2;
  • MMS-X;
  • Molbuild;
  • O;
  • ORTEP;
  • PLUTO;
  • PRXBLD;
  • Rings;
  • Script