[bug #22041] The PDB atom serial number is not respected by the structure.write_pdb user function. -- May 15, 2014 - 11:34

URL:
  <http://gna.org/bugs/?22041>

                 Summary: The PDB atom serial number is not respected by the
structure.write_pdb user function.
                 Project: relax
            Submitted by: bugman
            Submitted on: Thu 15 May 2014 09:34:57 AM UTC
                Category: relax's source code
Specific analysis category: None
                Priority: 5 - Normal
                Severity: 3 - Normal
                  Status: None
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.1.7
         Discussion Lock: Any
        Operating System: All systems

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Details:

The following commands, when run from the relax base directory in the prompt
UI mode, will demonstrate the problem:

pipe.create('pdb_merge_test', 'N-state')
structure.read_pdb('1RTE_trunc.pdb', dir='test_suite/shared_data/structures',
set_mol_name='N-dom')
structure.read_pdb('1RTE_trunc.pdb', dir='test_suite/shared_data/structures',
set_mol_name='C-dom')
structure.write_pdb('test', force=True)

The resultant file test.pdb has the contents:

REMARK   4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.                  
 
REMARK  40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).                       
 
HET    CYN  A 445       1                                                     
 
HET    CYN  B 445       1                                                     
 
HETNAM     CYN UNKNOWN                                                        
 
FORMUL   1  CYN    C1                                                         
 
ATOM      5  N   LEU A   3      49.617   4.693  46.426  1.00  0.00           N
 
ATOM      6 CA   LEU A   3      49.432   5.476  45.190  1.00  0.00           C
 
ATOM      7  C   LEU A   3      50.346   4.980  44.055  1.00  0.00           C
 
ATOM      8  O   LEU A   3      49.924   4.868  42.889  1.00  0.00           O
 
ATOM      9 CB   LEU A   3      49.673   6.968  45.457  1.00  0.00           C
 
ATOM     10 CG   LEU A   3      49.804   7.863  44.222  1.00  0.00           C
 
ATOM     11 CD1  LEU A   3      48.564   7.837  43.327  1.00  0.00           C
 
ATOM     12 CD2  LEU A   3      50.075   9.282  44.625  1.00  0.00           C
 
TER       9      LEU A   3                                                    
 
HETATM   10    C CYN A 445      29.160  13.127  62.533  1.00  0.00           C
 
ATOM      5  N   LEU B   3      49.617   4.693  46.426  1.00  0.00           N
 
ATOM      6 CA   LEU B   3      49.432   5.476  45.190  1.00  0.00           C
 
ATOM      7  C   LEU B   3      50.346   4.980  44.055  1.00  0.00           C
 
ATOM      8  O   LEU B   3      49.924   4.868  42.889  1.00  0.00           O
 
ATOM      9 CB   LEU B   3      49.673   6.968  45.457  1.00  0.00           C
 
ATOM     10 CG   LEU B   3      49.804   7.863  44.222  1.00  0.00           C
 
ATOM     11 CD1  LEU B   3      48.564   7.837  43.327  1.00  0.00           C
 
ATOM     12 CD2  LEU B   3      50.075   9.282  44.625  1.00  0.00           C
 
TER      19      LEU B   3                                                    
 
HETATM   20    C CYN B 445      29.160  13.127  62.533  1.00  0.00           C
 
MASTER        0    0    2    0    0    0    0    0   18    2    0    0        
 
END                                                                           
 

However the PDB convention is that the atom serial number starts at 1 and
sequentially increases for each ATOM, HETATM, and TER record.




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