[bug #21520] Failure of the structure.write_pdb user function if too many models, hence atoms, are present. -- January 20, 2014 - 17:11

URL:
  <http://gna.org/bugs/?21520>

                 Summary: Failure of the structure.write_pdb user function if
too many models, hence atoms, are present.
                 Project: relax
            Submitted by: bugman
            Submitted on: Mon 20 Jan 2014 04:11:38 PM GMT
                Category: None
                Severity: 3 - Normal
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: 3.1.3
        Operating System: All systems

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Details:

If too many atoms are present, the MASTER record creation fails with the error
about the MASTER record being too long.  The message with the debugging flag
turned on is:


Traceback (most recent call last):
  File "/data/relax/branches/double_rotor/prompt/interpreter.py", line 341, in
exec_script
    runpy.run_module(module, globals)
  File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
    fname, loader, pkg_name)
  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File
"/data/relax/branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/generate_distribution.py",
line 46, in <module>
    generate.run()
  File "../generate_base.py", line 77, in run
    self._create_distribution()
  File "../generate_base.py", line 229, in _create_distribution
    self.interpreter.structure.write_pdb('distribution.pdb', compress_type=2,
force=True)
  File "/data/relax/branches/double_rotor/prompt/uf_objects.py", line 221, in
__call__
    self._backend(*new_args, **uf_kargs)
  File "/data/relax/branches/double_rotor/pipe_control/structure/main.py",
line 1212, in write_pdb
    cdp.structure.write_pdb(file, model_num=model_num)
  File "/data/relax/branches/double_rotor/lib/structure/internal/object.py",
line 2709, in write_pdb
    pdb_write.master(file, num_het=len(het_data_coll),
num_coord=num_atom+num_hetatm, num_ter=num_ter, num_conect=num_conect)
  File "/data/relax/branches/double_rotor/lib/structure/pdb_write.py", line
1330, in master
    _record_validate(text)
  File "/data/relax/branches/double_rotor/lib/structure/pdb_write.py", line
85, in _record_validate
    raise RelaxError("The PDB record '%s' is too long." % record)
RelaxError: RelaxError: The PDB record 'MASTER        0    0    2    0    0   
0    0    0135000 1000    0    0          ' is too long.





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