[Chimera-users] Measure buried area

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 15 09:46:50 PST 2013


Hi Jian,
The first suggestion is to be very careful about what atoms you are specifying in the command, because it is very easy to accidentally include waters etc. that would make the calculation much more likely to fail. See the "measure buriedArea" description:
<<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>>

The only parameters available with "measure buriedArea" (that you can try changing) are:
(1) probeRadius
(2) vertexDensity
(3) the two sets of atoms defining the interface -- again be very careful, and in addition you may want to try deleting beforehand all the subunits that are not involved in the interface you are trying to measure.

Unfortunately there is no exact recipe for a fix; it is a rather unpredictable numerical failure. You might not find the right combination of parameters, or it might even work if you just use a different computer.  There is a general page about surface calculation failures and workarounds:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

However, please note that for "measure buriedArea" specifically, many of the suggestions in that page do not apply, because to do the measurement it has to use MSMS to calculate the surface of the two parts of the interface both together and apart.

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 Nov 15, 2013, at 9:23 AM, Jian Guan wrote:

> Hi all,
> I use measure command to calculate the buried area between capsomer and Fab. My input file is pentamer.pdb and Fab.pdb. I made surface model for them respectively and use the command line as shown below:
> measure buriedArea #3 #2 probeRadius 1.4
> However, it replied as “Surface calculation failed”
> I tried also delete all non-binding units in the pentamer, it still can not work.
> Does anyone know how to deal with that? Thank you so much.
> Sincerely yours,
> Jian




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