Re: CCL:holes in molecular surface when using mds from QCPE

 > When I convert the obtained the dots file into a displayable format I
 > find large holes in the surface calculated. I had a look in the source
 > code, but since I am mainly a perl and c++ programmer I couldn't find
 > anything obvious.
 > Has anyone observed something similar ?
 This may be an error in covering the surface with
 polygons, but sounds more like another phenomenon
 I know. If you are using a molecular surface of the type
 based on rolling a probe sphere over the protein
 (piecewise sphere and torus), then there
 are cases where real holes exist (well they look
 like holes, but are not actually holes in the surface,
 just pockets with atom-sized round entry holes).
 Consider the case of two protein atoms separated far enough
 apart that when you roll the probe sphere
 in contact with both atoms, you actually get a
 self-intersecting torus. Similar thing can happen
 with more than two protein atoms. Some programs
 generate cusps, leaving out the interpenetrating
 part (the right choice I think). Some may offer the
 option of filling these in, or even put both surfaces.
 They look bad, but they are places that a water molecule
 might actually go. If you tweak the probe radius up a little, they may
 go away if you need a pretty picture. From the standpoint
 of hydrophobicity, the cusps are rather important and can be
 seen in full atomistic simulations with water and methane.
 Richard Gillilan