[Chimera-users] SAS exposure question

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 17 14:08:06 PDT 2017


Hi Kyle,
When you have shown a molecular surface, the atoms and residues automatically get solvent-accessible surface area and solvent-excluded surface area attributes assigned, named “areaSAS” and “areaSES”, respectively.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

You can see histograms of all the values or write them out using the Render By Attribute tool (in menu under Tools… Structure Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

Or, if you just want to sum over a selected set of atoms or residues to get a single number out, you can do that with the Attribute Calculator tool (in menu under Tools… Structure Analysis).  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

For example, after calculating (and optionally hiding) a surface, I could select a bunch of residues 

Command: surface
Command ~surf
Command:  select #1:15-50.A,60-65.A

…..and get their total SASA by using Attribute Calculator to calculate a new attribute of “molecules” (since you only want 1 value per molecule model) with 

Formula:  sum(residue.areaSAS)

with the option to “Restrict attribute assignment to current selection” turned on, click Apply.  Then the Render by Attribute tool will pop up with the single value shown in the area that would normally be used for the histogram (if there were multiple values).

I would just do this for each model individually, since if you did it all at once it might be confusing as to which value goes with which model.
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

> On Apr 17, 2017, at 11:00 AM, Kyle Novakowski <kyle.novakowski at gmail.com> wrote:
> 
> Hi there,
> I'm hoping to get some clarification on how to calculate the SAS of a defined set of residues within a molecular structure. I currently have 3 molecular structures in a chimera file and was hoping to compare the SAS of a specific region within 2 mutant proteins relative to that same region of the wildtype protein.
> Thanks.
> Kyle




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