CCL: Connolly surface with hydrophobicity coloring

["Elaine Meng" <meng:-:cgl.ucsf.edu>]

 Sent to CCL by: "Elaine  Meng" [meng*cgl.ucsf.edu]
 Hi Andrew,
 In Chimera you can show the Connolly molecular surface colored by amino acid
 hydrophobicity -- it uses a lookup table of amino acid hydrophobicity values,
 however, and does not calculate a distance-dependent "potential".
 Hydrophobicity coloring is easily done by simply choosing the
 "hydrophobicity surface" option from the Presets menu, or with more
 steps you can customize the coloring. This tutorial includes an example:
 http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html
 Chimera is free for noncommercial use.
 http://plato.cgl.ucsf.edu/chimera/download.html
 For hydrophobicity "potential" calculations, you may want to take a
 look at the Platinum web server:
 http://model.nmr.ru/platinum/
 I hope this helps,
 Elaine
 -----
 Elaine C. Meng, Ph.D.
 UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco