[MMTK] MMTK Issue Grab Bag

[Rocco Moretti]

Hello all,

Three comments/questions, mainly aimed at the MMTK developers:

Issue 1
---------
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)[1]
    return int(round(density*(cell_volume-solute_volume)/solvent.mass()))

As you may note, the 'o' in the for loop is never used.

Is this the desired behaviour? Or is this a latent bug?

Issue 2:
---------

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 
within MMTK?

Issue 3:
--------

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.


Thanks,
-Rocco
 

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