[bug #21522] Incorrect atom count in the MASTER record for PDB files with multiple models. -- January 21, 2014 - 10:04

URL:
  <http://gna.org/bugs/?21522>

                 Summary: Incorrect atom count in the MASTER record for PDB
files with multiple models.
                 Project: relax
            Submitted by: bugman
            Submitted on: Tue 21 Jan 2014 09:04:40 AM GMT
                Category: relax's source code
                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:

The MASTER record created by the structure.write_pdb user function has the
incorrect number of ATOM and HETATM records in the MASTER record
(http://www.nmr-relax.com/api/3.0/lib.structure.pdb_write-module.html#master).
 For example, the following code:

pipe.create('PDB models', 'N-state')
structure.add_model(model_num=1)
structure.add_model(model_num=2)
structure.add_atom(atom_name='N', res_name='Pro', res_num=2, pos=[1., 2., 3.],
element='N')
structure.write_pdb('aaa.pdb', force=True)

Will produce the PDB file:

REMARK   4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.                  
 
REMARK  40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).                       
 
MODEL        1                                                                
 
ATOM      1  N   Pro     2       1.000   2.000   3.000  1.00  0.00           N
 
TER       2      Pro     2                                                    
 
ENDMDL                                                                        
 
MODEL        2                                                                
 
ATOM      1  N   Pro     2       1.000   2.000   3.000  1.00  0.00           N
 
TER       2      Pro     2                                                    
 
ENDMDL                                                                        
 
MASTER        0    0    0    0    0    0    0    0    2    2    0    0        
 
END                                                                           
 

The numCoord and numTer values of 2 should both actually be 1.




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