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Hey Jeff, Why not try the command line version of CAVER. It is easily adjustable and provides nice figures of solvent accessibility for Pymol. It also prints out a ton of stats in the log files if you want numbers. -Yarrow On Wed, Jun 25, 2014 at 1:10 PM, Jeff Holden <[log in to unmask]> wrote: > Experts, > > I would like to compare the substrate binding site of two homologous > proteins. Based on crystal structures it is clear that the substrate > binding site of protein A is more solvent exposed then protein B. > > Is there a way to measure the solvent exposure of the substrate in protein > A and B? Or perhaps you have an additional suggestion for making a > structural comparison (besides what seems obvious...noting the differences > in non-covalent interactions)? > > Thanks, > Jeff >