[Chimera-users] << measuring areas >>

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 2 08:54:46 PST 2013


Hi Hatuey,
Well…. yes and no.

If you can select the desired set of atoms, you can then sum their surface areas.  However, you cannot select surface triangles directly.  Further complications are (A) values are associated with surface points, not triangles, but points don't have areas
(B) electrostatic potential (ESP) coloring by default shows the potential not exactly at the surface but 1.4 angstroms farther out.  In other words, the solvent-excluded surface (SES) is displayed, but colored by the potential at the larger solvent-accessible surface (SAS).

So, you could select the *atoms* at which ESP is positive (or negative) and then get the total SAS and/or SES area for those atoms, but it would *not* be the same as the area of the surface with positive potential.   I don't know of any way to get the latter.  To do the former, after opening the structure and the ESP map and showing the surface, you would:

(1) use Values at Atom Positions (under Tools… Volume Data) to map ESP values onto atoms; this automatically opens Render/Select by Attribute 
(2) in Render/Select by Attribute, use the Select tab and select the desired set of atoms based on their potential values.  It will be difficult, however, to decide what set of values to choose.  This will select both buried and surface atoms, but buried atoms will not contribute to the total surface area calculated in the next step. 
(3) use Attribute Calculator (under Tools… Structure Analysis) to sum areaSAS or areaSES for atoms over the whole model.  For example, calculate attribute "totalSESpositive" for "molecules" (which really means models) with formula: sum(atom.areaSES)
and making sure to "restrict formula domain to current selection, if any" so that the sum will only include the selected atoms.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

Sorry it isn't  exactly what you wanted to do.  It's the closest thing I could come up with, however. I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 2, 2013, at 2:02 AM, Hatuey Hack <hatuey.hack at gmail.com> wrote:

> Hellos ChimeraUsers,
> It could be possible to measure different parts of a surface according to a given parameter?
> For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values.
> Best regards,
> Hatuey




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