[Chimera-users] Question about Measure Volume and Area

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 20:24:40 PDT 2008

Hi Patrick,

  You're hitting a bug in the solvent excluded surface calculation 
code.  With small probe radii you just get an outer surface and the 
inner surface is missing due to this bug.  With larger probe radii you 
get both the inner and outer surface.  With the correct two layers the 
volume is of course smaller since only the volume between the inner and 
outer layers is included.  And the surface area is of course larger.  
The easiest way to see this is to look at the clipped surface.  Use 
Favorites / Side View and move the front clip plane (left vertical 
yellow line) so it cuts the surface allowing you to see inside.  You can 
also look at how many connected surface components were found in the 
text output in Favorites / Reply Log.  Should be 2.

  By the way, the Chimera ring finding that is done to determine the vdw 
radii goes into a tail spin on your cage.  I deleted all the bonds to 
avoid that.


Patrick Redmill wrote:
> Hi all,
>    I am using the the calculate "Area and Volume" option in Chimera to 
> estimate the SASA and excluded volumes of a family of fullerene 
> materials. I need to calculate the area and volume using two different 
> probe sizes (1.4 and 2.0, to be specific). For most of my particles, 
> you see that the volume and area are relatively insensitive to a 
> change in probe size (which I would expect). For one particle, 
> however, I find the results to be quite different and unintuitive. For 
> instance:
> 1.4:
> Area: 1174
> Volume: 3534
> 2.0:
> Area: 1692
> Volume: 2493
> My (perhaps wrong??) assumption is that the area calculator uses a 
> Connolly algorithm. If that is the case, I can't understand why a 
> larger probe would give a larger area (smaller probes samples more 
> surface). Also, why would a larger probe give a larger volume? Again, 
> I thought the volume calculator used a Voronoi algorithm, which, to me 
> seems independent of probe size. Any idea what may be wrong about my 
> understanding? I've attached a .pdb of the molecule in question if 
> you'd like to take a gander. Thanks in advance!
> ~Patrick
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