[chimera-dev] [Chimera-users] Surface electrostatic and hydrophobicity.

[Miguel Ortiz Lombardia]

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 at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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