bugrelax - 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 codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.2.0Operating 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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.

 

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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Fri 01 Feb 2013 02:27:51 PM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
    Fri 01 Feb 2013 11:53:02 AM UTCbugmanCarbon-Copy-=>Added -unavailable-
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