SURFNET

One thing this program does very well is find the surface gaps and clefts (as well as interior voids) in a macromolecule. These gaps may be displayed in the CSB using O or RIBBONS. Below is an example of the gaps in the il8 dimer displayed with RIBBONS.

A description of how this figure was made.

The manual for SURFNET is available locally online.

To use SURFNET in the CSB do the following in a directory containing your PDB file:

setup surfnet (or source /srv/local/setup/surfnet.set)

This will deposit a file called surfnet.par in your working directory. Edit this file according to the manual.

Then type: surfnet

You will then have to decide how to display the surface net (which is in the form of a map). In the CSB the easiest options are PostScript, O, or RIBBONS. For the latter two options, first convert the map to O style with the following type of commands:

setup rave
mapman

MAPMAN > read map gaps.den ccp4
MAPMAN > mappage map gaps.map
MAPMAN > quit

Note: If you publish material created with SURFNET please cite the following:

Laskowski R. A. (1995) SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph., 13, 323-330.