[Chimera-users] Question about Measure Volume and Area

Patrick Redmill patrickredmill at gmail.com
Fri Aug 15 08:26:09 PDT 2008

Thanks guys!,
   What you're saying makes a lot of sense actually. Now that you mention
it, I am sure both surfaces are being measured. This is the fattest (closed)
particle I have, thus, it makes sense that the interior surface was measured
for that one but not the others. I'll definitely try out the "Measure and
Color Blobs" and "Area/Volume from the web." Thanks again!


On Thu, Aug 14, 2008 at 10:42 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Patrick,
> I'm having trouble getting a surface on that structure in the first place,
> but setting that issue aside...
> I guess you are using "Measure Volume and Area" since "Area/Volume from
> Web" does not have an option for probe radius 2.0.  As discussed on the
> "Measure Volume and Area" man page,
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/
> measurevol.html>
> this tool calculates the volume and area directly from the triangulated
> surface, not analytically.  However, the surface area values reported in the
> Reply Log as soon as you show a molecular surface are analytical, so use
> those, assuming you are able to successfully generate a surface.
> I can think of a couple possible explanations for nonintuitive results:
> (a) there is more than one surface component (disconnected blob) and
> "Measure Volume and Area" includes the total of both.  Maybe with one probe
> size it also calculates the inside surface, with the other it does not.  To
> make sure you are only measuring one component, use "Measure and Color
> Blobs" instead.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/
> pickblobs.html>
> (b) the surface calculation failed (maybe high symmetry makes this more
> likely?) and the triangulation was incomplete or artifactual.  Seems like
> this would be visible, however.
> Voronoi volume is a totally different thing than surface-enclosed volume.
>  Each atom is partitioned into a cell, essentially, and the surface atoms
> have infinite Voronoi volumes because there are no neighbors in the outside
> direction to bound their cells.  That being said, you can use "Area/Volume
> from Web" to calculate atomic Voronoi volumes. I think it reports -1 for the
> infinite volumes. You might also want to try calculating surface areas with
> that tool.  There are a few different allowed probe radii, but 2.0 is not
> one of the choices.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/
> surfvol.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html

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it's a nuclear show and the stars are gone
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