[Chimera-users] Question about Measure Volume and Area

Patrick Redmill patrickredmill at gmail.com
Thu Aug 14 17:43:23 PDT 2008


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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