bugrelax - Bugs: bug #20479, Model-free analysis failed in the...

 
 
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bug #20479: Model-free analysis failed in the GUI after setting the protocol mode to local tm.

Submitted by:  Stanislava Panova <stacy>
Submitted on:  Mon 04 Feb 2013 03:25:48 PM UTC  
 
Category: GUISpecific analysis category: None
Priority: 5 - NormalSeverity: 5 - Blocker
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.2.1Operating System: All systems

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(Jump to the original submission Jump to the original submission)

Tue 05 Feb 2013 07:29:52 AM UTC, SVN revision 18416:

Merged revisions 18414-18415 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18414 | bugman | 2013-02-04 22:34:03 +0100 (Mon, 04 Feb 2013) | 9 lines

Fix for bug #20479 - the failure of non-fully automated model-free analyses in the GUI.

This bug was reported by Stanislava Panova (https://gna.org/users/stacy) at
https://gna.org/bugs/?20479.

The problem is GUI specific and was when running each diffusion model one after the other. The GUI
was setting the base data pipe to the 'final' data pipe, which is a clear error.
........
r18415 | bugman | 2013-02-05 08:11:15 +0100 (Tue, 05 Feb 2013) | 3 lines

Added spherical diffusion to the optimisation in the Mf.test_bug_20479_gui_final_pipe GUI test.
........

(Browse SVN revision 18416)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 09:34:03 PM UTC, SVN revision 18414:

Fix for bug #20479 - the failure of non-fully automated model-free analyses in the GUI.

This bug was reported by Stanislava Panova (https://gna.org/users/stacy) at
https://gna.org/bugs/?20479.

The problem is GUI specific and was when running each diffusion model one after the other. The GUI
was setting the base data pipe to the 'final' data pipe, which is a clear error.

(Browse SVN revision 18414)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 09:30:27 PM UTC, comment #5:

This is a GUI only problem.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 05:50:12 PM UTC, SVN revision 18409:

Merged revisions 18406-18408 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r18406 | bugman | 2013-02-04 18:29:12 +0100 (Mon, 04 Feb 2013) | 3 lines

Copyright update.
........
r18407 | bugman | 2013-02-04 18:30:29 +0100 (Mon, 04 Feb 2013) | 3 lines

Docstring expansion for the State.test_bug_20480 GUI test.
........
r18408 | bugman | 2013-02-04 18:42:27 +0100 (Mon, 04 Feb 2013) | 5 lines

Created the Mf.test_bug_20479 GUI test to catch bug #20479 (https://gna.org/bugs/?20479).

This bug was reported by Stanislava Panova (https://gna.org/users/stacy).
........

(Browse SVN revision 18409)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 05:42:28 PM UTC, SVN revision 18408:

Created the Mf.test_bug_20479 GUI test to catch bug #20479 (https://gna.org/bugs/?20479).

This bug was reported by Stanislava Panova (https://gna.org/users/stacy).

(Browse SVN revision 18408)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 05:24:12 PM UTC, comment #2:

The fix for bug #20480 (https://gna.org/bugs/?20480) simplifies catching this bug. The attached state file can now be loaded, the model-free protocol mode changed to 'final', and clicking on 'Execute relax' triggers the bug.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 04 Feb 2013 03:32:35 PM UTC, comment #1:

Another problem is, that for some reasons I cannot load relax state, which I have saved prior to execution. It is giving me

RelaxError: The data pipe 'final' has not been created yet.

(file #17127)

Stanislava Panova <stacy>
Mon 04 Feb 2013 03:25:48 PM UTC, original submission:

I was trying to run model-free analysis of relaxation data: 4 files (R1, R2, NOE for 800 MHz and R2 for 600MHz). First I have chosen local tm model and executed relax. It has created local_tm directory with aic, tm0-tm9 folders with result.bz2 in every folder. Then as I don't have pdb file with structure, I have chosen sphere model and it returned error:

relax> results.write(file='results', dir='/home/stacy/PrtG/local_tm/aic', compress_type=1, force=True)
Opening the file '/home/stacy/PrtG/local_tm/aic/results.bz2' for writing.
Exception raised in thread.

Traceback (most recent call last):
File "/usr/local/relax-2.2.1/gui/analyses/execute.py", line 87, in run
self.run_analysis()
File "/usr/local/relax-2.2.1/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 "/usr/local/relax-2.2.1/auto_analyses/dauvergne_protocol.py", line 193, in _init_
switch(self.pipe_name)
File "/usr/local/relax-2.2.1/generic_fns/pipes.py", line 469, in switch
test(pipe_name)
File "/usr/local/relax-2.2.1/generic_fns/pipes.py", line 503, in test
raise RelaxNoPipeError(pipe_name)
RelaxNoPipeError: RelaxError: The data pipe 'final' has not been created yet.

P.S. The main steps:

I have tried calculate rotational correlation time and I failed. First of all
to describe main steps:
1)load sequence from NOE data file
2)check spin.name, spin.element, spin.isotope
3)load relaxation data: 4 files (R1, R2, NOE for 800 MHz and R2 for 600MHz)
3)sequence.attach_protons()
4)dipolar relaxation (as I don't have pdb file, I have skipped first part and
applyed only magnetic dipolar relaxation setup)
5)csa relaxation
6)protocol model local tm
7) execute relax
8)protocol sphere
9)execute relax

Stanislava Panova <stacy>

 

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Attach File(s):
   
   
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Attached Files
file #17127:  state.bz2 added by stacy (48kB - application/x-bzip)
file #17123:  NoeRelN added by stacy (2kB - application/octet-stream)
file #17124:  R2604 added by stacy (2kB - application/octet-stream)
file #17125:  R1850 added by stacy (2kB - application/octet-stream)
file #17126:  R2863 added by stacy (2kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by stacy (Submitted the item)
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    Follow 13 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 04 Feb 2013 09:34:46 PM UTCbugmanStatusIn Progress=>Fixed
      Open/ClosedOpen=>Closed
      Operating SystemGNU/Linux=>All systems
      SummaryModel-free analysis failed after creating local tm=>Model-free analysis failed in the GUI after setting the protocol mode to local tm.
    Mon 04 Feb 2013 09:30:27 PM UTCbugmanCategoryNone=>GUI
      StatusConfirmed=>In Progress
    Mon 04 Feb 2013 05:21:45 PM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
    Mon 04 Feb 2013 03:32:35 PM UTCstacyAttached File-=>Added state.bz2, #17127
    Mon 04 Feb 2013 03:25:48 PM UTCstacyAttached File-=>Added NoeRelN, #17123
      Attached File-=>Added R2604, #17124
      Attached File-=>Added R1850, #17125
      Attached File-=>Added R2863, #17126
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