[bug #22861] The chain IDs in the structure.write_pdb user function PDB files are incorrect after calling structure.delete. -- October 23, 2014 - 14:20

URL:
  <http://gna.org/bugs/?22861>

                 Summary: The chain IDs in the structure.write_pdb user
function PDB files are incorrect after calling structure.delete.
                 Project: relax
            Submitted by: bugman
            Submitted on: Thu 23 Oct 2014 12:20:45 PM UTC
                Category: relax's source code
Specific analysis category: All analyses
                Priority: 4
                Severity: 2 - Minor
                  Status: None
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.3.1
         Discussion Lock: Any
        Operating System: All systems

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Details:

The following user function calls demonstrate the problem:

pipe.create(pipe_name='PDB writing chainID fail', pipe_type='N-state')
structure.add_atom(mol_name='A', atom_name='N', res_name='Phe', res_num=1,
pos=[1.0, 1.0, 1.0], element='N')
structure.add_atom(mol_name='B', atom_name='N', res_name='Phe', res_num=1,
pos=[1.0, 1.0, 1.0], element='N')
structure.delete('#A')
structure.write_pdb('test.pdb', force=True)


The resultant PDB file contents are:

REMARK   4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.                  
 
REMARK  40                                                                    
 
REMARK  40 CREATED USING RELAX (HTTP://WWW.NMR-RELAX.COM).                    
 
REMARK  40                                                                    
 
REMARK  40 RELAX VERSION REPOSITORY CHECKOUT R26378                           
 
REMARK  40 SVN+SSH://BUGMAN@xxxxxxxxxxx/SVN/RELAX/TRUNK.                      
 
REMARK  40 CREATED ON THU OCT 23 14:15:12 2014.                               
 
ATOM      1  N   Phe B   1       1.000   1.000   1.000  1.00  0.00           N
 
TER       2      Phe B   1                                                    
 
MASTER        0    0    0    0    0    0    0    0    1    1    0    0        
 
END                                                                           
 

Note that the chainID is 'B' here, whereas by the PDB definition the chain IDs
are sequential and should start at 'A'.




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