Changes between Initial Version and Version 1 of SurfaceResidues

Timestamp:

Sep 8, 2020, 4:53:24 PM (6 years ago)

Author:

goddard

Comment:

--

SurfaceResidues

@@ +1 @@
+== 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