Hi Patrick, Thought I should mention that "Area/Volume from Web" (actually the Web server it accesses <http://helixweb.nih.gov/structbio/basic.html> ) is mainly parametrized to work on proteins, possibly nucleic acids. I would interpret the results with caution, as I don't know how it figures out the atom types (and thus VDW radii) in arbitrary molecules. On your structure, I tried the "Accessible surface (Gerstein)" option directly at the server, probe radius 1.4, and got values per atom plus this total: Chain X Residue Exposed Surface Area (Å2) 1 1918.02 (default probe radius is 1.4). Note "solvent-accessible surface" (SAS) area is where the center of the probe goes, not the same as the "solvent-excluded surface" (SES) comprised of probe contact and reentrant surface, and is expected to be much larger as it is a probe radius farther out. The surface in Chimera is the SES. Then I tried "Surfaces (MSMS)", probe radius 1.4, atoms+hetatms, and got this: ANALYTICAL SURFACE AREA : Comp. probe_radius, reent, toric, contact SES SAS 0 1.400 174.758 554.648 491.498 1220.904 1600.598 ... so this SES is fairly consistent with but larger than the value of 1174 you got in Chimera, probably because this server MSMS calculation used a larger VDW radius for the carbons. The SAS difference versus the Gerstein method is >300 - maybe the Gerstein calculation used an even larger VDW radius. Best, 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 On Aug 15, 2008, at 8:26 AM, Patrick Redmill wrote:
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