URL: <http://gna.org/bugs/?23295> Summary: PDB secondary structure HELIX and SHEET records not updated when merging molecules. Project: relax Submitted by: bugman Submitted on: Fri 20 Feb 2015 10:37:26 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 _______________________________________________________ Details: The structure.read_pdb user function <http://www.nmr-relax.com/manual/structure_read_pdb.html> fails to correctly update HELIX and SHEET secondary structure metadata in a PDB file when molecules are merged. The attached '2BE6_secondary_structure.pdb' file which contains the HELIX and SHEET records from the 2BE6 PDB file, as well as a few atoms from each of the 6 molecules, together with the attached 'test.py' relax script demonstrate the problem. For example the input HELIX record: HELIX 9 9 VAL D 1615 GLY D 1638 1 24 should be converted to: HELIX 9 9 VAL A 1615 GLY A 1638 1 24 as the molecule with the 'D' chain ID is merged into the molecule with the 'A' chain ID. However the merger does not modify the HELIX record. _______________________________________________________ File Attachments: ------------------------------------------------------- Date: Fri 20 Feb 2015 10:37:26 AM UTC Name: 2BE6_secondary_structure.pdb Size: 5kB By: bugman <http://gna.org/bugs/download.php?file_id=23876> ------------------------------------------------------- Date: Fri 20 Feb 2015 10:37:26 AM UTC Name: test.py Size: 388B By: bugman <http://gna.org/bugs/download.php?file_id=23877> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?23295> _______________________________________________ Message sent via/by Gna! http://gna.org/