[MMTK] Problems loading certain PDB files

Peter mmtk at maubp.freeserve.co.uk
Fri Jan 20 17:41:46 CET 2006


A couple of new problems for you.

I am using MMTK-2.5.13 under Python 2.3.3 on Windows XP.  I don't know 
what version of Scientific python I have - does it matter?

The following four PDB are all downloaded from www.rcsb.org

My only guess for what 'AE1', 'AE2', 'AD1' and 'AD2' mean is based on 
Appendix 3 of the format definition: "Atoms for which some ambiguity 
exists in the crystallographic results are designated A".  Are this 
probably Hydrogrens?

http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html

Thanks,

Peter

Problem One - Atom AE1 of PDB residue GLN
=========================================

import MMTK.Proteins
protein = MMTK.Proteins.Protein("5CYT.pdb", model="no_hydrogens")

PBD files known to cause this: 5CYT, 1ECO and 1VNS

Fails as follows:

Traceback (most recent call last):
   File "<pyshell#1>", line 1, in ?
     protein = 
MMTK.Proteins.Protein("c:/temp/ramachandran/top500/5CYT.pdb", 
model="no_hydrogens")
   File "c:\python23\Lib\site-packages\MMTK\Proteins.py", line 654, in 
__init__
     items = conf.createPeptideChains(model)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 170, in 
createPeptideChains
     chain = apply(Proteins.PeptideChain, (chain,), properties)
   File "c:\python23\Lib\site-packages\MMTK\Proteins.py", line 295, in 
__init__
     self._setupChain(circular, properties, conf)
   File "c:\python23\Lib\site-packages\MMTK\Biopolymers.py", line 79, in 
_setupChain
     conf.applyTo(self)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 33, in applyTo
     setResidueConfiguration(residue, self[i], pdbmap[0], altmap)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 313, in 
setResidueConfiguration
     raise IOError('Atom '+atom.name+' of PDB residue ' +
IOError: Atom AE1 of PDB residue GLN not found in residue Gln of object 
Gln12

Problem Two - Atom AD1 of PDB residue ASN
=========================================

import MMTK.Proteins
protein = MMTK.Proteins.Protein("451C.pdb", model="no_hydrogens")

Fails as follows:

Traceback (most recent call last):
   File "<pyshell#4>", line 1, in ?
     protein = 
MMTK.Proteins.Protein("c:/temp/ramachandran/top500/451C.pdb", 
model="no_hydrogens")
   File "c:\python23\Lib\site-packages\MMTK\Proteins.py", line 654, in 
__init__
     items = conf.createPeptideChains(model)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 170, in 
createPeptideChains
     chain = apply(Proteins.PeptideChain, (chain,), properties)
   File "c:\python23\Lib\site-packages\MMTK\Proteins.py", line 295, in 
__init__
     self._setupChain(circular, properties, conf)
   File "c:\python23\Lib\site-packages\MMTK\Biopolymers.py", line 79, in 
_setupChain
     conf.applyTo(self)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 33, in applyTo
     setResidueConfiguration(residue, self[i], pdbmap[0], altmap)
   File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 313, in 
setResidueConfiguration
     raise IOError('Atom '+atom.name+' of PDB residue ' +
IOError: Atom AD1 of PDB residue ASN not found in residue Asn of object 
Asn9




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