[MMTK] Problems loading certain PDB files

Eric Zollars zollars at caltech.edu
Fri Jan 20 17:54:27 CET 2006


In Asn and Gln the 'A' label indicates that the oxygen and nitrogen 
positions are ambiguous.

Eric

Peter wrote:
> 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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