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 Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.