[bug #14876] Error reading pdb file -- December 02, 2009 - 23:13

URL:
  <http://gna.org/bugs/?14876>

                 Summary:  Error reading pdb file
                 Project: relax
            Submitted by: michaelbieri
            Submitted on: Mittwoch 02.12.2009 um 22:13
                Category: relax's source code
                Severity: 3 - Normal
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: 1.3.4
        Operating System: GNU/Linux

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Details:

By executing the full_analysis.py script, I get an error message after
reading the pdb file (structure.read_pdb(PDB_FILE)). This does not occur
using the local_tm model.

This error occurs using relax 1.3.4 as well as the current 1.3 line. No error
occurs by running relax 1.3.3.


The error message is:

Internal relax PDB parser.
Opening the file '/home/michael/Desktop/LinuxBox/OMP/1F35_mono.pdb' for
reading.
RelaxWarning: The atom number 80 from the CONECT record cannot be found
within the ATOM and HETATM records.
RelaxWarning: The atom number 88 from the CONECT record cannot be found
within the ATOM and HETATM records.
Traceback (most recent call last):
 File "relaxGUI.py", line 4126, in exec_model_free
  start_model_free(self, which_model)
 File "relaxGUI.py", line 1533, in start_model_free
  Model()
 File "relaxGUI.py", line 1125, in __init__
  structure.read_pdb(PDB_FILE)
 File "/home/michael/Programme/relax-1.3/prompt/structure.py", line 464,
in read_pdb
  generic_fns.structure.main.read_pdb(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, parser=parser)
 File "/home/michael/Programme/relax-1.3/generic_fns/structure/main.py",
line 355, in read_pdb
  cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
 File
"/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
line 674, in load_pdb
  mol.fill_object_from_pdb(mol_records)
 File
"/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
line 1419, in fill_object_from_pdb
  self.atom_connect(index1=self.__atom_index(record[1]),
index2=self.__atom_index(record[i+2]))
 File
"/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
line 1378, in atom_connect
  if index2 not in self.bonded[index1]:
TypeError: list indices must be integers, not NoneType



Cheers
Michael



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File Attachments:


-------------------------------------------------------
Date: Mittwoch 02.12.2009 um 22:13  Name: 1F35_mono.pdb  Size: 106kB   By:
michaelbieri
pdb file. Monomer extracted using pymol
<http://gna.org/bugs/download.php?file_id=7430>

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