[MMTK] MMTK Issue Grab Bag

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Sep 16 15:20:03 CEST 2003

On Monday 15 September 2003 21:33, Rocco Moretti wrote:

>     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?

That's a bug. The argument of surfaceAndVolume should be "o" in both cases.

> 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?

No, or more precisely, there is no code in MMTK to do it. You can of course 
add your own code. MMTK can only construct positions for hydrogens, based on 
simple geometric criteria. The addition of sidechains would require a more 
specific knowledge about sidechain geometries. I suspect that the algorithms 
for this are not exactly trivial.

> Issue 3:
> --------
> Is there a compelling reason to output VRML version 1.0 code? At least on

It was the only one available when MMTK was first released, and then kept 
because no one ever requested a change. I wonder if anyone is using VRML that 
much nowadays. I don't even have a VRML browser installed any more, as none 
that I know for Linux are sufficiently stable and fast. In the good old days, 
I used VRweb, but that doesn't compile any more with recent  C++ compilers.

> 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

I was under the impression that any VRML browser would accept 1.0 as well.

If you prefer VRML2, just change "VRML." to "VRML2." everywhere in the module 
ConfigIO, and change the import at the beginning to VRML2 as well.

What is the general opinion of MMTK users on this? Should I make VRML2 the 

Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
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