[MMTK] about reading pdb files

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jun 10 13:28:58 CEST 2004


On Jun 10, 2004, at 9:45, Hua Wong wrote:

> If I get rid of coordinate at the end 60-336 (doesn't change the order 
> of the atoms coordinate) it seems to pass
>
> If I get rid of coordinate at the beginning of the file (1-20) I get 
> multiple errors

Those errors have nothing to do with the PDB file itself, but with the 
fact that by default MMTK assumes peptide chains to be terminated, i.e. 
have N-terminus and C-terminus forms of the amino acids at the two 
ends. If you edit out the first residue, then your chain starts with a 
standard amino acid instead of the N-terminal form. As a consequence, 
the atom names don't match with MMTK's expectations and you get the 
error message you describe.

You can use such files by specifying the options n_terminus=0 and/or 
c_terminus=0 when creating the MMTK objects. However, as Peter pointed 
out, it is easier to read in the whole file (MMTK.PDB.PDBConfiguration) 
and then modify the resulting configuration object.

Konrad.
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