[Chimera-users] Calculating surface for modified pdb file

[Elaine Meng]

Hi,
This is a commonly asked question. Please see this discussion of molecular surface calculation errors in Chimera and several possible workarounds:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

Another possible workaround is to use ChimeraX instead of Chimera.  ChimeraX reports SASA only (not SESA) but doesn’t get the failures like Chimera because it uses a different surface calculation method.  It’s easy in ChimeraX, you would just open the pdb file and then use a command something like:

measure sasa #1
- or -
measure sasa protein
(…to use protein atoms only, if there were other atoms like solvent that shouldn’t be included in the area calculation)

Above I was answering generally.  However, there may be some problems with your specific structure.  If it’s just the small PDB shown in text window upper right and in the graphics window, you can see 7 atoms in the 3D structure but 10 ATOM lines of text.  Looking at the text more closely there are two pairs of atoms that are exactly in the same X,Y,Z coordinates and that may be messing up the calculation.  Even if you eliminate one of each pair that’s still 8 lines of text for 7 atoms shown in the window.  I guess HA is not displayed in the window.  Did you want hydrogens included in the calculation?  Often people do not include hydrogen atoms when calculating macromolecular surface areas, but if you are treating this as a small molecule you might want them.  If not, you could just delete them all before showing surface. However, I don’t know if removing the 2 duplicate atoms and/or the hydrogens would make the calculation work.  You’d have to try it.

I hope this helps,
Elaine
—— 
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 29, 2018, at 9:38 AM, 김민재 <kjh950429 at gmail.com> wrote:
> 
> Hi y'all,
> I've been trying to calculate the surface area of a modified pdb file. It is an extracted part from 3hgn. Although the file seems pretty small and simple, I keep getting a miscalculation-due-to-huge-chain error message from Chimera. I think it's because of the "WARNING: treat_rs_edge: third atom not found for edge 7 9" lines that get recorded on the reply log.I'm new to Chimera and using pdb files, so I would really appreciate advice on how to solve this issue. I took everything in a screen shot below. I can send anyone the actual files if they want to take a closer look.
> Thanks.
> <2018-09-30.png>