[chimerax-users] Calculation of polar and apolar surface area

[Elaine Meng]

Hi Scott,
Your commands measure SASA for surfaces actually enclosing the specified atoms, not the macromolecule SASA.  Instead you want to (virtually) generate the SASA of the protein, and then use the “sum” option to get the contributions of the respective atoms to that protein surface.

Also your specifications with “@“ mean atom name, not element.  So you would only get the carbons named C, not all the others.

I think you want these commands instead:

measure sasa protein sum N | O | S
measure sasa protein sum C

measure sasa:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>

atom specification by element or other built-in classification:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin>

Now, whether/how to define polar or nonpolar surface area is a separate judgment call, but using element is one of several reasonable approaches.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 2, 2019, at 8:16 AM, Gorman, Scott Daniel <sdg176 at psu.edu> wrote:
> 
> Hi All,
> 
> I was wondering if anyone has a preferred way of calculating the polar and apolar surface areas for a macromolecule with ChimeraX? I've tried deleting all of the solvent and then using the command "measure sasa @N @O @S" for the polar surface area and then "measure sasa @C" for the apolar surface area, but the calculation for either comes up with a number too close to the total surface area, i.e. apolarSASA + polarSASA > totalSASA. So clearly I'm not approaching this problem correctly.
> 
> Scott Gorman
> PhD Candidate
> Boehr Lab
> PSU Chemistry