relax - Bugs: bug #20470, The unnumbered spin name 'H'... [Gna!]

relax - Bugs: bug #20470, The unnumbered spin name 'H'...

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bug #20470: The unnumbered spin name 'H' already exists.

Submitted by:	Edward d Auvergne <bugman>
Submitted on:	Fri 01 Feb 2013 11:47:57 AM UTC

Category:	relax's source code	Severity:	3 - Normal
Priority:	5 - Normal	Status:	Fixed
Privacy:	Public	Assigned to:	Edward d Auvergne <bugman>
Originator Name:		Open/Closed:	Closed
Release:	2.2.0	Operating System:	All systems

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Fri 01 Feb 2013 02:55:03 PM UTC, SVN revision 18354: Merged revisions 18350-18352 via svnmerge from svn+ssh://bugman@svn.gna.org/svn/relax/trunk ........ r18350 \| bugman \| 2013-02-01 15:23:45 +0100 (Fri, 01 Feb 2013) \| 6 lines Created the Structure.test_alt_loc_missing system test. This is to test that the internal relax PDB reader raises an error when a PDB file is encountered with alternate location indicators but the alt_loc argument has not been specified. ........ r18351 \| bugman \| 2013-02-01 15:27:36 +0100 (Fri, 01 Feb 2013) \| 7 lines Fix for bug #20470 (https://gna.org/bugs/?20470). The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate location indicator to read. This is used by the internal PDB reader. The bug was caught by the Structure.test_bug_20470_alternate_location_indicator system test. ........ r18352 \| bugman \| 2013-02-01 15:37:30 +0100 (Fri, 01 Feb 2013) \| 5 lines Fix for the checking of the alternate location indicator in the internal PDB reader. These checks now only occur for the ATOM and HETATM records. ........ (Browse SVN revision 18354)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 02:52:58 PM UTC, SVN revision 18353: Merged revisions 18349 via svnmerge from svn+ssh://bugman@svn.gna.org/svn/relax/trunk ........ r18349 \| bugman \| 2013-02-01 13:08:27 +0100 (Fri, 01 Feb 2013) \| 5 lines Created the Structure.test_bug_20470_alternate_location_indicator system test to catch bug #20470. This report is at https://gna.org/bugs/?20470. ........ (Browse SVN revision 18353)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 02:29:24 PM UTC, comment #4: For more discussions, see http://thread.gmane.org/gmane.science.nmr.relax.user/1387	Edward d Auvergne <bugman>
Fri 01 Feb 2013 02:27:36 PM UTC, SVN revision 18351: Fix for bug #20470 (https://gna.org/bugs/?20470). The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate location indicator to read. This is used by the internal PDB reader. The bug was caught by the Structure.test_bug_20470_alternate_location_indicator system test. (Browse SVN revision 18351)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 12:08:27 PM UTC, SVN revision 18349: Created the Structure.test_bug_20470_alternate_location_indicator system test to catch bug #20470. This report is at https://gna.org/bugs/?20470. (Browse SVN revision 18349)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 12:01:01 PM UTC, comment #1: The problem is the PDB ATOM record "Alternate location indicator". In the 1OGT PDB entry, there are alternate locations for a few amino acids. The internal relax PDB parser cannot currently handle this and it sees two residues. For example for residue 40, this causes the @N extraction to create two nitrogen spin containers for the single residue. The sequence.attach_protons user function can then not handle this. A temporary solution is to use the ScientificPython PDB parser.	Edward d Auvergne <bugman>
Fri 01 Feb 2013 11:47:57 AM UTC, original submission: This was reported on the relax users mailing list (see http://thread.gmane.org/gmane.science.nmr.relax.user/1387). The following instructions from the post trigger the bug: create a data pipe inside relax (pipe.create) get 1OGT.pdb and load by > structure.read_pdb('./1OGT.pdb', read_mol=1) load amide nitrogens: > structure.load_spins(spin_id='@N', ave_pos=True) attach protons > sequence.attach_protons()	Edward d Auvergne <bugman>

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Date	Changed By	Updated Field	Previous Value	Replaced By
Fri 01 Feb 2013 02:27:51 PM UTC	bugman	Status	None	Fixed
		Open/Closed	Open	Closed
Fri 01 Feb 2013 11:53:02 AM UTC	bugman	Carbon-Copy	-	Added -unavailable-

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