Hi Andrew, regarding hydrophobicity coloring, we use the rTools from Kristian Rother. http://www.rubor.de/bioinf/pymol_extensions.html The coloring schemes are according to http://www.expasy.org/cgi-bin/protscale.pl It comes with a nice user interface, or on command prompt you would simply do something like color_protscale 10, selection where 10 is the coloring scheme (might differ in your installation): Normalized consensus hydrophobicity scale. Eisenberg D., Schwarz E., Komarony M., Wall R. J. Mol. Biol. 179:125-142(1984).
(See also attached image) Cheers, Andreas Andrew D. Fant wrote:
Afternoon all,
I apologize if this has been hashed over on the list in the past. I haven't
been keeping up like I used to.
Is there a good way to calculate and color residues by hydrophobicity in
pymol? A google search showed only a very simple script that was based entirely
on a single-residue lookup table. I'm looking at a set of structure
predictions, and it would be nice to easily see that a fold exposes a large
patch of hydrophobic surface to solvent.
Thanks,
Andy
-- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de
<<inline: hydrophobicity.jpg>>
