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
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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:
HELIX9 9 VAL D 1615 GLY D 1638 1 24
should be converted to:
HELIX9 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.
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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
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