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. Tom 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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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! ~Patrick On Thu, Aug 14, 2008 at 10:42 PM, Elaine Meng <meng@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@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

-- My office glows all night long it's a nuclear show and the stars are gone Elevator, elevator, take me home

Hi Patrick, The calculation of volume enclosed in the triangulated surface is trivial. I just choose any point (say the first vertex of the surface), then sum up the volumes of the tetrahedrons formed by that point and each triangle face making up the surface. (Some of those tetrahedrons are inverted and have negative volume.) This gives the exact volume enclosed in the surface which is defined by triangles. One small catch is that I need to check that the surface has no holes since then the volume is not well-defined. For a solvent excluded surface there will be no holes. Tom Patrick Redmill wrote:

Hey guys, One more quick question. Is there a non-trivial calculation associated with the surface enclosed volume? Or is it just a numerical integration between the surfaces? If it's non-trivial, is there a good ref for the algorithm? Thanks!

~Patrick