Programs for representing the surface of a channel inside protein: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 4: | Line 4: | ||
2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php | 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/ | 3. HOLE. http://d2o.biop.ox.ac.uk:38080/ | ||
Revision as of 06:08, 29 August 2008
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.