Molecular Surfaces
6. Molecular Surface Graphics

Michael L. Connolly

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

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E-mail: connolly@best.com



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

Before there was fast hardware rendering of polyhedra, molecular surfaces were rendered in software. Early examples include: (Quarendon, 1984) and (Connolly, 1983a, 1985a). The molecular surface of crambin is shown below, with the convex spherical patches colored yellow, the saddle-shaped pieces of tori colored green, and the concave reentrant surface colored blue.

Rendering volumetric data in molecular systems has produced some beautiful images (Goodsell, Mian and Olson, 1989). Michael B. Prisant of Duke University has used ray tracing to render geometric aspects of protein structure. Addison-Wesley's electronic publishing has a nice virus image.

Plotting of protein molecular surfaces has the advantage that it is easier to publish than rendered images (Connolly, 1986b). Below is the surface of superoxide dismutase, drawn as a stack of planar contours with hidden-line elimination.

The University of Wisconsin virology laboratories has produced some nice topographical maps of viruses.

Interactive graphics is the best way to visualize molecular surfaces. Busetta, Tickle and Blundell (1983) developed a program called DOCKER that used the molecular surfaces of Pearl and Honegger (1983). At U.C.S.F. a program for computing van der Waals surfaces on the fly was developed (Bash, Pattabiraman, Huang, Ferrin and Langridge, 1983). Early molecular modeling software displayed surfaces computed externally, usually by MS. Molecular modeling software developed by Andrew Dearing (of Shell) while at the U.C.S.F., originally named Chem, and then MOGLI, has been taken over by Evans and Sutherland and renamed PSSHOW. At the Scripps Research Institute Molecular Graphics Laboratory a molecular modeling front-end for GRAMPS (O'Donnell and Olson, 1981) was developed and named GRANNY (Connolly and Olson, 1985). The GRAMPS acronym stands for GRAphics for the Multi-Picture System. The Evans and Sutherland Multi-Picture System was a calligraphic display popular during the 1980's. It excelled at drawing lines and dots. Here is an example of a tripeptide surface made up of curved lines. The coloring is according to shape.

Biosym's Insight (Dayringer, Tramontano, Sprang and Fletterick, 1986) molecular modeling program displays molecular surfaces. It was originally developed as a collaboration between the U.C.S.F. Biochemistry and Biophysics Department and Monsanto (St. Louis) and named Proteus (Dayringer, Tramantano and Fletterick, 1986). The Insight program supports dotted molecular surfaces: Solvent-Accessible Surfaces. The Ribbons program (Carson and Bugg, 1986; Carson, 1987; Carson, 1991) developed at the University of Alabama, also has the ability to display molecular surfaces. Molecular surface splines can be displayed by MANOSK (Cherfils, Vaney, Morize, Surcouf, Colloc'h and Mornon, 1988). The WHATIF program of Gert Vriend (1990) can display polyhedral molecular surfaces.

More recently, writers of molecular modelling software have developed their own surface-generating routines. The Darmstadt group has developed software to both compute and display (MOLCAD) molecular surfaces (Heiden, Reiling, Vollhardt, Zachmann and Brickmann, 1995). The most widely used software for computing and displaying polyhedral molecular surfaces is the GRASP program written by Anthony Nicholls of Barry Honig's laboratory at Columbia University (Physicians & Surgeons campus). At University College, London the SURFNET program (Laskowski, 1995) both computes and displays molecular surfaces. In Finland the SCARECROWprogram of Leif Laaksonen (1991, 1992), while primarily developed to display molecular dynamics simulation results, also computes and displays molecular surfaces. At the Scripps Research Institute AVS (Advanced Visualization Systems) software (Upson, Faulhaber, Kamins, Laidlaw, Schlegel, Vroom, Gurwitz and van Dam, 1989) is used for molecular modelling (Duncan, Pique and Olson, 1993; Duncan, Macke and Olson, 1995).

Various physical chemical properties can be mapped onto the molecular surface and color-coded (Chapman, 1993). This is usually done for a polyhedral molecular surface with physical-chemical values assigned to each vertex and interpolated over each triangle. The best known example is the electrostatic potential coloring of GRASP (Nicholls, Bharadwaj and Honig, 1993; Honig and Nicholls, 1995). The Darmstadt group has argued that texture mapping, with its banded appearance, is superior to interpolating colors continuously for each triangle (Heiden, Schlenkrich and Brickmann, 1990; Teschner, Henn, Vollhardt, Reiling and Brickmann, 1994). Texture mapping has also been applied by Duncan and Olson (1995b). Methods for displaying protein surface motions and structural uncertainty have been developed (Duncan and Olson, 1995a; Altman, Hughes and Gerstein, 1995).

Some beautiful molecular surface images can be found in a beautiful country, Switzerland: University of Geneva (Jacques Weber), and University of Basel (Real-Time Isocontouring).

[ 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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