[Chimera-users] Question about Measure Volume and Area

[Elaine Meng]

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