[Chimera-users] Calculation of SASA with probe size of 0.8Å

[Elaine Meng]

Hi Amy,
It sounds like you may be using the "Area/Volume from Web" tool in Chimera, which in turn uses the StrucTools web server at NIH.  In that case, you are limited to the options that the server provides.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html>

However, you do not need to use that tool in Chimera to get SASA.  If you can just display a molecular surface for your protein in Chimera, you will automatically get the area of both the SES (solvent-excluded surface = molecular surface, corresponding to what is displayed) and the SAS.  Both totals are reported in the Reply Log (under Favorites in the menu). If your protein has hydrogens, the surfaces will include them.  "Components" means disconnected parts, so if values are reported for more than one component, you may want to use only the largest.  The others are generally interior bubbles.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

Surface calculation parameters such as probe radius can be changed by selecting the surface (Ctrl-click), opening the Selection Inspector (for example by clicking the green magnifying glass at the bottom right of the Chimera window), and in that dialog inspecting "MSMS surface" and changing the values.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop>

Note: sometimes surface calculation fails numerically.  If it fails but still shows the surface you expect, the failure is for the interior bubbles only, and you can proceed if you didn't need the surface areas to include those. However, in some cases you may not get any surface or values reported.  Using a small probe may make such failures more likely.  In the case of complete failure, see:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html>

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 Sep 20, 2012, at 5:20 PM, Amy Davenport wrote:

> Hi all,
> I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8Å to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated.
> Thank you,
> Amy Davenport Migliori
> UCSD