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@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