[Chimera-users] Calculating SAS and SES with Chimera-MSMS wrap

Jaime Rodríguez-Guerra jaime.rogue at gmail.com
Mon Apr 7 08:44:01 PDT 2014

Dear Chimera dev team,

I am trying to use your MSMS wrapper to compute some SAS/SES values for a
given set of atoms. As suggested in a previous post in this list, I've
taken a look into Measure.measure.buried_area() and I think I've got it,
but just wanted to make sure.

Here is my current procedure:

import chimera, Measure, MoleculeSurface
atoms = chimera.selection.currentAtoms()
xyzr_data = Measure.measure.atom_xyzr(atoms)
surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data)

for i, a in enumerate(atoms):
    print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0],


Is this OK? I don't know how to handle all that output that MSMS is giving

Thanks in advance,
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