[MMTK] problem reading PDB files with hydrogens

konrad.hinsen at laposte.net konrad.hinsen at laposte.net
Fri May 27 11:30:03 CEST 2005


On May 26, 2005, at 16:33, Andrew J. Bordner wrote:

> I would like to read PDB files while ignoring hydrogen atom 
> coordinates.  MMTK seems to throw an exception for non-standard 
> hydrogen atom names even when model = 'no_hydrogens'.  It would 
> probably be better for the PDB file parser to just skip hydrogen atoms 
> rather that checking their names when model = 'no_hydrogens' or 
> 'none'.

The PDB file parser doesn't know what you intend to do with its output. 
However, you can throw away the hydrogens explicitly by adding one line 
to your code:

>
> An example is PDB entry 7RSA":
>
> conf = MMTK.PDB.PDBConfiguration('7rsa')
conf.deleteHydrogens()
> molecules = conf.createPeptideChains('no_hydrogens')
>
> IOError: Atom 1H of PDB residue LYS not found in residue Lys of object 
> .Lys1

That should remove the IOError.

Konrad.
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