[Chimera-users] Selecting only protein surfaces programmatically

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 20 09:23:25 PDT 2017


Hi Ashton,
The “measure distance” command gives the shortest distance between one set of atoms and/or surface pieces and another set of atoms or surface pieces. However, this may not help you because you can’t specify only using the surface of a specific atom; the entire molecular surface is one piece and can only be specified as a whole.  You might be able to use some of the code from that command’s implementation, however.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

Further, as you have discovered, Chimera is limited in ways you can specify surface models or surface pieces: only as a model number or as a selection, as described at the bottom of this page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#othermodels>

Here is a tricky command to select models that are not atomic models (select models and not atoms):

sel # &~ @

I can’t advise on python details, but I believe that everything that can be run as a Chimera command can be python-ified by the general mechanism described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 Jun 19, 2017, at 2:00 PM, Ashton Omdahl <aomdahl at gmail.com> wrote:
> 
> Chimera friends-
> I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line?
> Thanks!
> Ashton
>  



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