Molecular Surfaces
4. Molecular Graphics

Michael L. Connolly

1259 El Camino Real, #184
Menlo Park, CA 94025
U.S.A.

The Author's Web page
The Author's software web page
E-mail: connolly@best.com



http://www.netsci.org/Science/Compchem/feature14.html

The history of molecular graphics falls readily into two parts:

  • B.C. (Before Connolly)
  • A.D. (After Dots)

This section describes the early years of molecular graphics, before the molecular dot surfaces, and also more recent parts of molecular graphics not directly pertaining to molecular surfaces.

The earliest efforts to model molecules and electron density were made in Project MAC at M.I.T. (Langridge and MacEwan, 1965; Levinthal, 1966; Barry, Levinthal, Ward and Zwick, 1968). The acronym MAC stands for Mathematics And Computation. This research group is now called Switzerland. The people involved in this early molecular modeling work moved on to other locations, where they continued their molecular modeling efforts (Meyer, 1971; Barry and North, 1971; Katz and Levinthal, 1972; Levinthal, Wodak, Kahn and Dadivanian, 1975; Langridge, 1974; Collins, Cotton, Hazen, Meyer, and Morimoto, 1975). The early systems, because of hardware limitations, generally could model only small molecules and not proteins.

With the advent of raster graphics displays, line drawings were supplemented by hard sphere, CPK-type images. Several methods for rendering such models have been developed (Porter, 1978; Feldmann, Bing, Furie and Furie, 1978; Max, 1979; Palmer, Hausheer and Saxe, 1989; Evans, 1993). The RasMol program (Sayle and Bissel, 1992) draws hard-sphere images with shadows. At Scripps they have developed a light-weight molecular modeling program for X-Windows called Flex (Pique, Macke and Arvai, 1991). The UNC computer scientists, in collaboration with scientists at Duke University (Surles, Richardson, Richardson and Brooks,1994), have developed SCULPT, a program that has real-time energy calculations as the protein conformation changes. The Chapel Hill people have also developed virtual reality methods for feeling atoms (Taylor II, Robinett, Chi, Brooks, Wright, Williams and Snyder, 1993)

An early molecular plotting program was ORTEP, the Oak Ridge Thermal Ellipsoid Program of Carroll Johnson (1976). During the eighties programs for drawing the secondary structure of proteins were developed (Lesk and Hardman, 1982; Lesk and Hardman, 1985; Lesk, 1991). One of the main programs currently used for plotting protein structures is the Molscript program of Per Kraulis (1991).

In order to view supplementary material to the journal Protein Science, the reader can use the kinemage program (Dave Richardson and Jane Richardson, 1992; Richardson and Richardson, 1994). Recently, the Open Inventor graphics software of Silicon Graphics (Wernecke, 1994) has been adapted to both molecular modeling (Molecular Inventor: Henn, Benzel, Engel and Teschner (1995)) and the world-wide web (Virtual Reality Modeling Language: Bell, Parisi and Pesce, 1995). Robinson and Hardy (1995) have developed a VRML program called Builder. At the Imperial College London Chemistry Department, Henry Rzepa (Spedding and Hargreaves, 1996) has developed some interactive molecular visualization called an EyeChem Collaboratory. See also the work of the Darmstadt group: 3D Molecular Graphics on the World Wide Web.

There are a number of academic software distribution sites and commercial molecular modeling vendors:

Silicon Graphics maintains a list of molecular modeling software that runs on their hardware. Catalytica also maintains a list of molecular graphics packages. And the National Institutes of Health maintain a list of Molecular Biology Software. The main journal for molecular graphics is the Journal of Molecular Graphics. Recently, there has also been established an online journal, the Journal of Molecular Modeling . Related journals include the Journal of Computational Chemistry, the Journal of Computer-Aided Molecular Design, the Journal of Computational Biology , the Journal of Molecular Biology , and the Journal of Mathematical Chemitry. The American Chemical Society has a web page on color graphics in their journals. The Association for Computing Machinery (ACM) also has a web page on their computer graphics special interest group (ACM SIGGRAPH).

There are a number of beautiful molecular images on the world wide web:

In spite of the convenience of computers, some artists have chosen to produce protein illustrations by hand (Dickerson and Geis, 1969; Dickerson and Geis, 1983; Richardson, 1985).

[ 1. Introduction ] [ 2. Physical Molecular Models ] [ 3. Electron Density Fitting ] [ *** 4. Molecular Graphics *** ] [ 5. Solvent-Accessible Surfaces ] [ 6. Molecular Surface Graphics ] [ 7. Molecular Volume and Protein Packing ] [ 8. Shapes of Small Molecules and Proteins ] [ 9. Structure-based Drug Design ] [ 10. Protein-Protein Interactions ] [ 11. Surface Biology, Chemistry and Physics ] [ 12. Bibliography ]

All material in ths article Copyright © 1996 by Michael L. Connolly



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