bugrelax - Bugs: bug #20613, Failure of the model-free...

 
 
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bug #20613: Failure of the model-free auto-analysis when creating the diffusion tensor PDB representation.

Submitted by:  Angelo <angelof>
Submitted on:  Wed 13 Mar 2013 01:42:20 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: 2.2.2Operating System: All systems

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Wed 13 Mar 2013 02:21:51 PM UTC, SVN revision 18813:

Merged revisions 18812 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18812 | bugman | 2013-03-13 15:21:07 +0100 (Wed, 13 Mar 2013) | 10 lines

Fix for bug #20613 (https://gna.org/bugs/?20613), the failure of the diffusion tensor PDB creation.

This was reported by Angelo Miguel Figueiredo .

The problem was that the diffusion tensor PDB representation structure.create_diff_tensor_pdb user
function was being called even when the local tm global model was selected. This naturally failed
as there is no global diffusion tensor. Now this user function is avoided for the local tm global
model.
........

(Browse SVN revision 18813)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 13 Mar 2013 02:21:07 PM UTC, SVN revision 18812:

Fix for bug #20613 (https://gna.org/bugs/?20613), the failure of the diffusion tensor PDB creation.

This was reported by Angelo Miguel Figueiredo .

The problem was that the diffusion tensor PDB representation structure.create_diff_tensor_pdb user
function was being called even when the local tm global model was selected. This naturally failed
as there is no global diffusion tensor. Now this user function is avoided for the local tm global
model.

(Browse SVN revision 18812)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 13 Mar 2013 02:14:02 PM UTC, SVN revision 18811:

Merged revisions 18810 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18810 | bugman | 2013-03-13 15:13:33 +0100 (Wed, 13 Mar 2013) | 14 lines

Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test to catch bug #20613.

This was reported by Angelo Miguel Figueiredo at
https://gna.org/bugs/?20613.

This test is a direct copy of the Mf.test_bug_20563_missing_ri_error system test. The only change
is that the local tm global model results file (in the local_tm/aic/ directory) has been modified.
This results were read into relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb
loaded into the data pipe, and the results saved again.

This triggers the bug as the problem is the presence of structural data with the local tm global
model being selected in the auto-analysis.
........

(Browse SVN revision 18811)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 13 Mar 2013 02:13:33 PM UTC, SVN revision 18810:

Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test to catch bug #20613.

This was reported by Angelo Miguel Figueiredo at
https://gna.org/bugs/?20613.

This test is a direct copy of the Mf.test_bug_20563_missing_ri_error system test. The only change
is that the local tm global model results file (in the local_tm/aic/ directory) has been modified.
This results were read into relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb
loaded into the data pipe, and the results saved again.

This triggers the bug as the problem is the presence of structural data with the local tm global
model being selected in the auto-analysis.

(Browse SVN revision 18810)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 13 Mar 2013 01:42:20 PM UTC, original submission:

Dear Edward,

Many thanks for your reply.

The original bug details:

relax> structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb', dir='/home/final', force=True)
Exception raised in thread.

Traceback (most recent call last):
File "/home/angelo/Software/relax-2.2.2/gui/analyses/execute.py", line 87, in run
self.run_analysis()
File "/home/angelo/Software/relax-2.2.2/gui/analyses/auto_model_free.py", line 808, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, diff_model=self.data.global_models, mf_models=self.data.mf_models, local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, conv_loop=self.data.conv_loop)
File "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py", line 234, in _init_
self.execute()
File "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py", line 745, in execute
self.write_results()
File "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py", line 937, in write_results
self.interpreter.structure.create_diff_tensor_pdb(file="tensor.pdb", dir=dir, force=True)
File "/home/angelo/Software/relax-2.2.2/prompt/uf_objects.py", line 219, in _call_
self._backend(*new_args, **uf_kargs)
File "/home/angelo/Software/relax-2.2.2/generic_fns/structure/geometric.py", line 449, in create_diff_tensor_pdb
raise RelaxNoTensorError('diffusion')
RelaxNoTensorError: RelaxError: No diffusion tensor data exists.

In the .txt file attached is my relax --info.

Unfortunately, I didn't get any log files or information saying which model best fits my data and surprisingly the rex.txt file is empty (see also in attach an example) but in the grace directory it seems to have values?!
As a pdb structure I've used a NMR model ensemble.

Once again, thanks for your help.

Angelo <angelof>

 

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Attached Files
file #17426:  myrelax_info.txt added by angelof (6kB - text/plain)
file #17427:  rex.txt added by angelof (20kB - text/plain)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by angelof (Submitted the item)
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    Follow 9 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed 13 Mar 2013 02:22:11 PM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Wed 13 Mar 2013 02:07:38 PM UTCbugmanCategoryNone=>relax's source code
    Wed 13 Mar 2013 02:07:32 PM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
      Operating SystemGNU/Linux=>All systems
      Summarycreate diffusion tensor=>Failure of the model-free auto-analysis when creating the diffusion tensor PDB representation.
    Wed 13 Mar 2013 01:42:20 PM UTCangelofAttached File-=>Added myrelax_info.txt, #17426
      Attached File-=>Added rex.txt, #17427
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