[MMTK] Exception in findHydrogenPositions()

Peter mmtk at maubp.freeserve.co.uk
Sun Jan 22 19:26:44 CET 2006

This works perfectly:

 >>> import MMTK.Proteins
 >>> protein = MMTK.Proteins.Protein("1HMP.pdb", model="calpha")

If I try this with the "no hydrogens" model then I get a warning message:

 >>> protein = MMTK.Proteins.Protein("1HMP.pdb", model="no_hydrogens")
Warning: Some atoms in a protein have undefined positions.

On the other hand, using the default model I just get an exception error:

 >>> protein = MMTK.Proteins.Protein("1HMP.pdb")
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/usr/lib/python2.4/site-packages/MMTK/Proteins.py", line 654, 
in __init__
     items = conf.createPeptideChains(model)
   File "/usr/lib/python2.4/site-packages/MMTK/PDB.py", line 172, in 
   File "/usr/lib/python2.4/site-packages/MMTK/ChemicalObjects.py", line 
804, in findHydrogenPositions
     raise ValueError('position of ' + a.fullName() + \
ValueError: position of .Leu101.sidechain.C_delta_1 is undefined

I'm guessing that findHydrogenPositions() is trying to position the 
hydrogens attached to this ambiguous Leucine residue.

Why doesn't this simply give the warning about atoms with undefined 
positions (in this case, the carbon atom in Leu101, AND the hydrogens 
attached to it)?


P.S. Konrad - Did you get the Windows MMTK installation programs?

More information about the mmtk mailing list