[MMTK] MMTK Issue Grab Bag
roccomoretti at netscape.net
Mon Sep 15 16:33:30 CEST 2003
Three comments/questions, mainly aimed at the MMTK developers:
The Solvation module (MMTK version 2.2) seems to bog down (if not
outright hang up) when dealing with a universe containing more than one
item. I've tracked it down to a suspicious loop in
numberOfSolventMolecules(), and a similar construct in addSolvent():
solute_volume = 0.
for o in universe._objects:
solute_volume = solute_volume + surfaceAndVolume(universe)
As you may note, the 'o' in the for loop is never used.
Is this the desired behaviour? Or is this a latent bug?
Is there a way to add missing heavy atoms to a protein? I'm dealing with
PDB files that lack sidechain atoms on some residues. I know that Swiss-
PDB-Viewer can reconstruct the sidechains. Is it possible to do it from
Is there a compelling reason to output VRML version 1.0 code? At least on
windows, the majority of the free VRML viewers I've found work with VRML
version 2.0 only, and refuse to display VRML 1.0. This is only a minor
annoyance at its worst, and if there is a specific program/platform you
are maintaining compatability with, then I understand.
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