bugrelax - Bugs: bug #21522, Incorrect atom count in the MASTER...

 
 
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bug #21522: Incorrect atom count in the MASTER record for PDB files with multiple models.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Tue 21 Jan 2014 09:04:40 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: 3.1.3Operating System: All systems

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Tue 21 Jan 2014 09:35:16 AM UTC, SVN revision 22038:

Merged revisions 22034 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22034 | bugman | 2014-01-21 10:30:24 +0100 (Tue, 21 Jan 2014) | 10 lines

Fix for bug #21522 (https://gna.org/bugs/?21522) and bug #21520 (https://gna.org/bugs/?21520).

These bugs are the structure.write_pdb user function creating an incorrect MASTER record and the
failure of the structure.write_pdb user function when creating the MASTER record due to too many
ATOM and HETATM records being present.

The counts for the ATOM, HETATM, and TER records are now only for a single model, rather than being
the sum for all models together.
........

(Browse SVN revision 22038)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 21 Jan 2014 09:31:30 AM UTC, SVN revision 22035:

Merged revisions 22031 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22031 | bugman | 2014-01-21 10:15:22 +0100 (Tue, 21 Jan 2014) | 11 lines

Created the Structure.test_bug_21522_master_record_atom_count system test.

This is designed to catch bug #21522 (https://gna.org/bugs/?21522), the structure.write_pdb user
function creating an incorrect MASTER record. This hence also catches bug #21520
(https://gna.org/bugs/?21520), the failure of the structure.write_pdb user function when creating
the MASTER record due to too many ATOM and HETATM records being present.

The test simply creates to structural models, adds one atom, and writes out a PDB file, checking its
contents.
........

(Browse SVN revision 22035)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 21 Jan 2014 09:30:24 AM UTC, SVN revision 22034:

Fix for bug #21522 (https://gna.org/bugs/?21522) and bug #21520 (https://gna.org/bugs/?21520).

These bugs are the structure.write_pdb user function creating an incorrect MASTER record and the
failure of the structure.write_pdb user function when creating the MASTER record due to too many
ATOM and HETATM records being present.

The counts for the ATOM, HETATM, and TER records are now only for a single model, rather than being
the sum for all models together.

(Browse SVN revision 22034)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 21 Jan 2014 09:15:23 AM UTC, SVN revision 22031:

Created the Structure.test_bug_21522_master_record_atom_count system test.

This is designed to catch bug #21522 (https://gna.org/bugs/?21522), the structure.write_pdb user
function creating an incorrect MASTER record. This hence also catches bug #21520
(https://gna.org/bugs/?21520), the failure of the structure.write_pdb user function when creating
the MASTER record due to too many ATOM and HETATM records being present.

The test simply creates to structural models, adds one atom, and writes out a PDB file, checking its
contents.

(Browse SVN revision 22031)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 21 Jan 2014 09:06:46 AM UTC, comment #1:

Bug #21520 (https://gna.org/bugs/?21520) is triggered by this bug.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 21 Jan 2014 09:04:40 AM UTC, original submission:

The MASTER record created by the structure.write_pdb user function has the incorrect number of ATOM and HETATM records in the MASTER record (http://www.nmr-relax.com/api/3.0/lib.structure.pdb_write-module.html#master). For example, the following code:

pipe.create('PDB models', 'N-state')
structure.add_model(model_num=1)
structure.add_model(model_num=2)
structure.add_atom(atom_name='N', res_name='Pro', res_num=2, pos=[1., 2., 3.], element='N')
structure.write_pdb('aaa.pdb', force=True)

Will produce the PDB file:

REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
REMARK 40 CREATED BY RELAX ([HTTP://WWW.NMR-RELAX.COM]).
MODEL 1
ATOM 1 N Pro 2 1.000 2.000 3.000 1.00 0.00 N
TER 2 Pro 2
ENDMDL
MODEL 2
ATOM 1 N Pro 2 1.000 2.000 3.000 1.00 0.00 N
TER 2 Pro 2
ENDMDL
MASTER 0 0 0 0 0 0 0 0 2 2 0 0
END

The numCoord and numTer values of 2 should both actually be 1.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.

 

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    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 21 Jan 2014 09:36:23 AM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
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