View source for Programs for representing the surface of a channel inside protein

The following programs can be used for representing the surface of a channel inside protein.

# PASS
# Pymol with Caver scripts: http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php
# HOLE. http://d2o.biop.ox.ac.uk:38080/
# CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera
# MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php
# HOLLOW. http://hollow.sourceforge.net/.
# The program O can this with following protocol
#*  1/ make object of solvents in the tunnel, sel_off, sel_prop, sel_vis, sphere centred on tunnel...
#* 2/ mask from these solvents, ncs_mask_sph, ncs_mask_lay
#* 3/ asa of just protein
#* 4/ copy space group info from an electron density map to the asa 'map'
#* 5/ average the asa map, using the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel.
# use CAVENV to identify the channel and confirm the channel by solving the structure of Xenon-pressured crystals - see "Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase" (Tzanko I. Doukov, Leah C. Blasiak, Javier Seravalli, Stephen W. Ragsdale, and Catherine L. Drennan) http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/2008/47/i11/abs/bi702386t.html