[MMTK] PDBOutputFile creates files unreadeable for PDBConfiguration

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jun 8 12:41:19 CEST 2006


On May 30, 2006, at 21:55, jak at biogeo.uw.edu.pl wrote:

> Seems that the reason is that HETATM lines for carbon atoms get  
> substituted with ATOM, which upon reading gives IOError: Atom C of  
> PDB residue DC not found...

The reason is a different one, and in fact I am surprised that you  
don't have more problems with your PDB file. According to the PDB  
file format, each atom in a residue should have a unique atom name.  
In your file, there is a single residue with multiple atoms called  
"C", "H", etc.

I have changed the way MMTK handles PDB residues with non-unique atom  
names, because the current behaviour is really just a side effect of  
the absence of any decent treatment. However, the modified behaviour  
won't solve your problem: MMTK will write out your AtomCluster as 19  
separate residues. But at least the new behaviour is predictable, and  
produces only standard-conforming PDB files.

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil, Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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