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 som
>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
