[MMTK] Correct Hydrogens

[Stuart Murdock]

Hi

I have PDB formatted files (for proteins) which have some missing 
hydrogen atoms. I would like
 to be able to read them into MMTK from the PDB file without the correct 
additional hydrogens being
introduced by MMTK. I would like to analyse sub-sections of proteins 
with MMTK, which are not the
complete molecule.

I can currently do this by simply not performing the

chain.findHydrogenPositions()

statement in the file PDB.py when creating peptide chains and deleting 
any undefined atoms, but was
wondering if there was a cleaner way of doing this without editing any 
files.

Any suggestions would be great.

Thanks,

Stuart
  

-- 

Stuart Murdock Ph.D,
Research Fellow,
Dept. of Chemistry / E-Science,
University of Southampton,
Highfield, Southampton,
SO17 1BJ, United Kingdom
 
http://www.biosimgrid.org