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
_______________________________________________________
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.
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?22041>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
