== Surface Exposed Residues ==

Here is how to select surface exposed residues that are hydrophobic.

Use [http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa measure sasa] to define an "area" attribute of residues, then assign residue hydrophobicities from a file with the [http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html defattr] command, and then use a single [http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes select] command to intersect these two attributes.  

In the [http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html#examples defattr example files] I already happened to include a file kdHydrophobicity.txt to assign Kyte-Doolittle hydrophobity, as well as for several other hydrophobicity scales.  Just download whichever one(s) you want.

The commands could be something like:

{{{
open 6g2j
measure sasa protein
defattr ~/Desktop/kdHydrophobicity.txt
select ::area>25 & ::kdHydrophobicity>0.0
surface protein enclose protein
color sel magenta
}}}

... which looks like this ... 

[[Image(6gj2_kd.png)]]

... in pretty good agreement with MLP coloring, e.g.


{{{
mlp surfaces #1.3
}}}

[[Image(6gj2_mlp.png)]]

In the select command you may want to experiment with the surface-area and hydrophobicity cutoffs, as well as which hydrophobicity scale you use.  I didn't try a lot of values for surface-area cutoff, but here is with all residues with values >25 colored red, reasonable at least as a first approximation:

[[Image(6gj2_exposed.png)]]

Elaine Meng