SURFNET Operating Manual

1. Introduction

The SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file. It can compute:-

van der Waals surfaces
Gaps between molecules
Clefts and cavities
3D density distributions

Outputs

The surfaces computed by SURFNET are output in a number of formats for printing or for display/rendering on a graphics terminal using:-

• AVS* - (Advanced Visual Systems Inc., Waltham, MA, USA)
• CCP4 - (Collaborative Computational Project, Number 4, 1994)
• FRODO - (Jones, 1978)
• Insight II - (Molecular Simulations Inc., Burlington, MA, USA)
• O - (Jones et al., 1991)
• PostScript* - (Adobe Systems Inc., 1985)
• QUANTA - (Molecular Simulations Inc., Burlington, MA, USA)
• RASMOL* - (Sayle & Milner-White, 1995)
• Raster3D* - (Bacon & Anderson, 1988; Merritt & Murphy, 1994 )
• SYBYL - (Tripos Associates, Inc., St Louis, MO, USA)

* Note that, for the asterisked output formats (namely, PostScript, RASMOL, AVS and Raster3D) you need to run the SURFACE and SURFPLOT programs after running SURFNET.

A flow chart showing how these programs relate to the SURFNET programs is given in Appendix A.

Related programs

i. SURFACE and SURFPLOT

Two programs closely associated with SURFNET are SURFACE and SURFPLOT which are required for generating output files for Raster3D, RASMOL, or PostScript plots.

• SURFACE - Computes 3D contours from the .srf-format files generated by SURFNET, writing out files in .grf-format for input by SURFPLOT

• SURFPLOT - Reads in the .grf-format files generated by SURFACE and writes out:-
  • PDB-format files for input by RASMOL
  • .r3d-format files for input into Raster3D to generate ray-traced images, or
  • PostScript files for viewing on a PostScript viewer, or printing on a laser printer.

The programs are run in succession after SURFNET has been run.

See Viewing the SURFNET surfaces.

ii. Other surface-generation programs

There are a number of other programs that generate various kinds of surfaces for display by any of the above graphics programs:-

• GENBOX - Generates a box of the specified location and dimensions. (Useful for defining regions of interest for the related program, X-SITE).
• PLANE - Generates a plane from the supplied equation of a plane.
• CURVE - Generates plane-, paraboloid- or cubic-surfaces from the supplied equation.

See Planes, paraboloids and boxes.

iii. Map-manipulation programs

The map-manipulation programs allow the .srf files generated by SURFNET, or by any of the surface-generation programs above, to be modified, truncated, and compared:-

• MASK - Extracts only the required contour regions from a given .srf file. (Useful for extracting, say, just a protein's binding site from a map of all its clefts and cavities).
• CUTSRF - Cuts a given .srf file in the x-, y-, z-directions, as required, to reduce a given map to the size required.
• MAPDIFF - Compares two given .srf map files and either outputs a single map of their common regions, or else two separate maps of their differences. (Useful for, say, comparing the differences/similarities in the shapes of two protein binding sites).

See Extracting and comparing gap regions.

SURFNET Operating Manual