[MMTK] problem reading PDB files with hydrogens

Andrew J. Bordner bordner at ornl.gov
Thu May 26 16:33:00 CEST 2005


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'.

An example is PDB entry 7RSA":

conf = MMTK.PDB.PDBConfiguration('7rsa')
molecules = conf.createPeptideChains('no_hydrogens')

IOError: Atom 1H of PDB residue LYS not found in residue Lys of object .Lys1


   Regards,
      Andrew Bordner



More information about the mmtk mailing list