bugrelax - Bugs: bug #21097, structure.create_diff_tensor_pdb...

 
 
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bug #21097: structure.create_diff_tensor_pdb fails

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Tue 03 Sep 2013 03:37:14 PM 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: 3.0.0Operating System: All systems

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Tue 03 Sep 2013 03:42:19 PM UTC, SVN revision 20778:

Merged revisions 20776 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r20776 | bugman | 2013-09-03 17:40:26 +0200 (Tue, 03 Sep 2013) | 6 lines

Fix for bug #21097 (https://gna.org/bugs/?21097).

This was a simple typo. It has not been encountered before because it is in a rarely encountered
RelaxError.
........

(Browse SVN revision 20778)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 03 Sep 2013 03:41:40 PM UTC, comment #2:

This was simply a typo in a RelaxError. The fix will be part of the official relax 3.0.1 release.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 03 Sep 2013 03:40:26 PM UTC, SVN revision 20776:

Fix for bug #21097 (https://gna.org/bugs/?21097).

This was a simple typo. It has not been encountered before because it is in a rarely encountered
RelaxError.

(Browse SVN revision 20776)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 03 Sep 2013 03:37:14 PM UTC, original submission:

I noticed some kind of strange error when trying to generate a tensor PDB. I can reproduce this by opening an arbitrary results file and then this happens:

relax> structure.create_diff_tensor_pdb(scale=1.7999999999999999e-06, file='tensor.pdb', dir=None, force=False)
Calculating the centre of mass.
Traceback (most recent call last):
File "/opt/relax-3.0.0/gui/interpreter.py", line 303, in run
apply(fn, args, kwds)
File "/opt/relax-3.0.0/pipe_control/structure/main.py", line 199, in create_diff_tensor_pdb
com = pipe_centre_of_mass()
File "/opt/relax-3.0.0/pipe_control/structure/mass.py", line 94, in pipe_centre_of_mass
com, mass = centre_of_mass(pos=coord, elements=element_list)
File "/opt/relax-3.0.0/lib/structure/mass.py", line 62, in centre_of_mass
warn(RelaxWarning("Skipping the atom '%s' as the element '%s' is unknown." % (id, element)))
NameError: global name 'element' is not defined

Martin Ballaschk <mab>

 

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    Follow 4 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 03 Sep 2013 03:41:40 PM UTCbugmanStatusNone=>Fixed
      Assigned toNone=>bugman
      Open/ClosedOpen=>Closed
      Operating SystemGNU/Linux=>All systems
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