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

Tom Goddard goddard at sonic.net
Mon Apr 7 17:34:59 PDT 2014

Hi Jaime,

  Your Chimera code for reporting SES and SAS areas looks almost right.  It appears you have reversed SES and SAS though.  My look at the Chimera measure.py code says atom_areas[i,0] is SES area and atom_areas[i,1] is SAS area for atom i where atom_areas = surfaces[3].  You print them out switched.  Also I ran your code and SAS should be larger for most atoms, but it is smaller for most when using your code.

  Also be aware that your code completely ignores all non-selected atoms.  You are not getting the exposed areas of the selected atoms within the entire molecule.  Instead what your code calculates is the exposed area assuming all the non-selected atoms were deleted.  If instead you want the exposed areas taking into account the area buried by unselected atoms, then you need to do the atom_xyzr() call with all the atoms, and then just pick out the exposed areas for the selected atoms.


On Apr 7, 2014, at 8:44 AM, Jaime Rodríguez-Guerra wrote:

> 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], surfaces[3][i,1])
> ```
> Is this OK? I don't know how to handle all that output that MSMS is giving back! 
> Thanks in advance,
> Jaime.
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