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.

1. PASS.

2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php

3. HOLE. http://d2o.biop.ox.ac.uk:38080/

4. CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera

5. MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php.

6. HOLLOW. http://hollow.sourceforge.net/.

7. 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.