VMD-L Mailing List

From: Oliver Beckstein (oliver_at_biop.ox.ac.uk)
Date: Wed Mar 17 2004 - 04:45:45 CST

> I was wondering if anyone had a script or knew of a way to visualize the
> output from the program HOLE with VMD.

This will not be very helpful, I am afraid, but I _know_ of a way to have
HOLE produce beautiful VMD surfaces. Only, this requires two programs
called 'sos_triangle' and 'sph_process', which were (re)written by Guy
Coates (now at the Sanger Institute, Cambridge). Supposedly, they are in
the latest distribution of HOLE, so you might have to contact Oliver
Smart. I have only got binaries which I cannot distribute.

For what it's worth, once you've got these then the basic procedure is the
following:

hole < hole.input
sph_process -dotden 15 -colour -sos hole.sph hole.sos
sos_triangle -s -v < hole.sos > surf.vmd

vmd -e surf.vmd -m molec.pdb

where hole.sph is the 'SPHPDB' file produced by running HOLE with the
appropriate input on molec.pdb.

A template for the hole.input file that I use on a properly z-aligned
molec.pdb is the following (I process this with m4 and some other gimmicks
so just get rid of dnl's and substitute your parameters):

---------------------------------------------------------
dnl $Id: hole.m4,v 1.4 2003/12/10 11:29:38 oliver Exp $
dnl This is a template file for HOLE
dnl As long as you can see this note in the file it has
dnl not been properly processed by Makefile.hole and m4.
dnl (If you want to use it manually delete lines starting with `dnl')
COORD M4_INPUT_PDB
PLTOUT M4_NAME`'_hole.qpt
SPHPDB M4_NAME`'_hole.sph
MOLQPT M4_NAME`'_stick.qpt
RADIUS M4_RADIUSDB
CVECT M4_CVECTOR
CPOINT M4_CBOX
SAMPLE 0.20
ENDRAD 22
DOTDEN M4_DOTDENSITY
IGNORE SOL HOH K NA CL
------------------------------------------

Oliver 

-- 
Oliver Beckstein * oliver_at_biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/