Hi Miguel, I meant there is nothing like that *in Chimera*. It is available elsewhere, as you pointed out. You could add it as a feature request (just be aware it will be one of many!). It would be useful to include those links in the request. Also, if you know of different approaches, say different equations, that other people have used to calculate hydrophobic potential, we would be interested in them too. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 29, 2011, at 3:08 AM, Miguel Ortiz Lombardia wrote:
Le 28/01/2011 20:37, Elaine Meng a écrit :
and there is nothing like a "hydrophobic potential"
Dear Elaine,
In fact, such a thing does exist, have a look here:
http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html
and here:
http://www.moldiscovery.com/docs/vsplus/grid.html
I tried long ago to import GRID maps to Chimera but faced two problems:
1/ GRID did not provide a real "volume object", but one that would actually have non-zero values only on grid points corresponding to the solvent accessible surface, which is not implemented in Chimera (and the vdwdefine +1.4 trick is not good enough here)
2/ Eventually, GRID became part of a big package that needed a big licence fee...
How this potential is calculated was published long ago (see the second web page above and Goodford's cite in the first one) It would be truly useful if it was implemented in Chimera (if you still have slots in your wish-list) I can enter a feature request if you want...
Best regards, -- Miguel