[Chimera-users] Help SASA

[Elaine Meng]

Hi Andrea,
Oh, in that case we have a page describing different possible workarounds (not just “split”):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

However, these workarounds are mostly for display purposes rather than calculating SASA.  Solution #2 might work but is unpredictable, since there lots of different parameters you could try changing, and none of them are guaranteed to make the calculation work.  If it works, the area would be reported in the Reply Log, but it would be slightly different than the area that would be obtained with default parameters.

Given these issues, I recommend just using ChimeraX to get the SASA instead of Chimera.  It uses a different surface calculation that doesn’t have these numerical failures.   It’s pretty easy in ChimeraX; commands would be something like:

open 4hhb
measure sasa protein

(or, you can open a local file instead of giving a PDB ID).

UCSF ChimeraX (see Download link on left)
<http://www.rbvi.ucsf.edu/chimerax/index.html>

… ChimeraX measure command:
<http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html>

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 25, 2018, at 1:55 AM, Andrea Yimena Cardona Barreto <aycardonab at unal.edu.co> wrote:
> 
> The point is that I want to obtein the SASA, it returns code 5 and recomends to use the comand split, but I want to obtein the surface of the complete protein, not the surface of each subunit and don't know how to do that.
> 
> Thank you again
> 
> El mié., 24 oct. 2018 3:00 p. m., Elaine Meng <meng at cgl.ucsf.edu> escribió:
> Hi Andrea,
> What is the question?  You need to be a little more specific about what you tried and/or what problems you had, because it is too difficult to guess which part you don’t understand. 
> 
> If you show a molecular surface, then the surface area will automatically be reported in the Reply Log, which can be shown from the Favorites menu.
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 24, 2018, at 12:49 PM, Andrea Yimena Cardona Barreto <aycardonab at unal.edu.co> wrote:
> > 
> > Good afternoon,
> > 
> > my name is Andrea Cardona and I´m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I´m interested in obtain the  surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help?
> > 
> > -- 
> > Andrea Yimena Cardona Barreto
> > Maestría en Genética Humana
> > Universidad Nacional de Colombia