<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Jaime,<div><br></div><div> 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.</div><div><br></div><div> 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.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br><div><div>On Apr 7, 2014, at 8:44 AM, Jaime Rodríguez-Guerra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div><div><div><div><div><div><div>Dear Chimera dev team,<br></div><div><br></div>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.<br>
<br></div>Here is my current procedure:<br><br>```<br></div><div><span style="font-family:courier new,monospace">import chimera, Measure, MoleculeSurface<br></span></div><span style="font-family:courier new,monospace">atoms = chimera.selection.currentAtoms()<br>
</span></div><span style="font-family:courier new,monospace">xyzr_data = Measure.measure.atom_xyzr(atoms)<br></span></div><span style="font-family:courier new,monospace">surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data)<br>
<br></span></div><span style="font-family:courier new,monospace">for i, a in enumerate(atoms):<br></span></div><span style="font-family:courier new,monospace"> print "Atom: {0}, SAS: {1}, SES: {2}".format(<a href="http://a.name/">a.name</a>, surfaces[3][i,0], surfaces[3][i,1])</span><br>
<br>```<br><br></div>Is this OK? I don't know how to handle all that output that MSMS is giving back! <br><br></div>Thanks in advance,<br>Jaime.<br></div>
_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>