[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.

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:

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:

I hope this helps,
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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