URL:
http://gna.org/bugs/?23288
Summary: Failure of the structure.read_pdb user function when
simultaneously merging multiple molecules from one file.
Project: relax
Submitted by: bugman
Submitted on: Tue 17 Feb 2015 08:43:02 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 3 - Low
Severity: 2 - Minor
Status: None
Assigned to: bugman
Originator Name:
Originator Email:
Open/Closed: Open
Release: 3.3.6
Discussion Lock: Any
Operating System: All systems
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Details:
The following two user function calls are sufficient to trigger this bug when
running relax from the relax base directory:
pipe.create(pipe_name='merge test', pipe_type='N-state')
structure.read_pdb(file='2BE6_core_I_IV.pdb',
dir='test_suite/shared_data/structures', read_mol=[1, 3], set_mol_name='CaM
A', merge=True)
This results in the error:
Internal relax PDB parser.
Opening the file 'test_suite/shared_data/structures/2BE6_core_I_IV.pdb' for
reading.
Traceback (most recent call last):
File console, line 1, in module
File /data/relax/relax-trunk/prompt/uf_objects.py, line 225, in __call__
self._backend(*new_args, **uf_kargs)
File /data/relax/relax-trunk/pipe_control/structure/main.py, line 1099, 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,
alt_loc=alt_loc, verbosity=verbosity, merge=merge)
File /data/relax/relax-trunk/lib/structure/internal/object.py, line 2084,
in load_pdb
new_mol_name.append(set_mol_name[mol_index])
IndexError: list index out of range
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