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A recipe for reading surfaces from Roman Laskowski's SURFNET program (for finding cavities in macromolecules) into PyMol for visualisation.

1. Create your surfaces in "CCP4" format in SURFNET.

A. The "endianness" of SURFNET is set to big endian by default - see the 
remarks about the SGI flag.  Change this if you're on a little endian machine, 
e.g. LINUX/i386.
B.SURFNET can be compiled against ccp4 version 5 and 6 libraries 
by following the instructions in the SURFNET distribution and modifiying 
the link lines at the end of ccp4link.scr to replace 



$CLIB/libccp4f.a $CLIB/libccp4c.a

2. Use Gerard Kleywegt's mapman from the USF RAVE package to convert the CCP4 density map to XPLOR format

e.g. in a shell on LINUX:

$ lx_mapman

MAPMAN > READ map1 gaps.den

MAPMAN > WRITE map1 gaps.xplor XPLOR 

3. Open the XPLOR map in PyMol

4. Generate a mesh or surface object from the map using isomesh or isosurface.

e.g. on the PyMol command line:

isomesh gaps_mesh, gaps, 100.0