bugrelax - Bugs: bug #20198, Relaxation data back-calculation...

 
 
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bug #20198: Relaxation data back-calculation from model-free parameters fails.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Tue 25 Sep 2012 10:20:27 AM UTC  
 
Category: NoneSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.1.1Operating System: All systems

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Tue 16 Oct 2012 08:25:22 AM UTC, SVN revision 17831:

Merged revisions 17552-17580 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r17552 | bugman | 2012-09-25 13:42:50 +0200 (Tue, 25 Sep 2012) | 7 lines

Fix for bug #20198 (https://gna.org/bugs/?20198) - the relaxation data back-calculation error.

The problem was that the call to the model-free overfit_deselect() method was deselecting any spins
lacking relaxation data! This should not happen, as no spins need to have relaxation data for this
calculation.
........
r17553 | bugman | 2012-09-25 14:03:50 +0200 (Tue, 25 Sep 2012) | 5 lines

Added the data_check Boolean argument to all of the specific analysis overfit_deselect() methods.

This allows the unit tests to pass.
........
r17554 | bugman | 2012-09-25 14:05:41 +0200 (Tue, 25 Sep 2012) | 7 lines

Added a tryptophan NE1 data set to the sphere model-free model test data.

This is in preparation to catch bug #20197 (https://gna.org/bugs/?20197).

The scripts have also been updated for the newer relax designs.
........
r17555 | bugman | 2012-09-25 14:38:21 +0200 (Tue, 25 Sep 2012) | 6 lines

Improved the model-free overfitting deselection printouts prior to optimisation.

Only a single message per spin is now given when the spin is deselected, minimising the amount of
output.
........
r17556 | bugman | 2012-09-25 14:53:03 +0200 (Tue, 25 Sep 2012) | 3 lines

More improvements to the model-free over-fitting deselection printouts.
........
r17557 | bugman | 2012-09-25 14:58:22 +0200 (Tue, 25 Sep 2012) | 5 lines

Printouts for the over-fitting deselection of spins are suppressed for the back-calculation of relaxation data.

This affects the model-free Monte Carlo simulations, simplifying the output.
........
r17558 | bugman | 2012-09-25 15:01:37 +0200 (Tue, 25 Sep 2012) | 3 lines

All overfit_deselect() methods now accept and use the verbose argument.
........
r17559 | bugman | 2012-09-25 15:06:25 +0200 (Tue, 25 Sep 2012) | 3 lines

The overfit_deselect() printouts are now regularised and match the model-free printouts.
........

[...] r17560 | bugman | 2012-09-25 15:18:23 +0200 (Tue, 25 Sep 2012) | 6 lines

[...]

[...] Small change to the sphere model model-free test suite data.

[...]

[...] The trptophan indole data is now merged into the last residue (a glycine) to catch bug #20197

[...] (https://gna.org/bugs/?20197).

[...]........

[...] r17561 | bugman | 2012-09-25 15:21:43 +0200 (Tue, 25 Sep 2012) | 5 lines

[...]

[...] Modified the Mf.test_dauvergne_protocol system test to catch bug #20197 (https://gna.org/bugs/?20197).

[...]

[...] The sphere test data NE1 and HE1 data is now being used in this system test, triggering the bug.

[...]........

[...] r17562 | bugman | 2012-09-25 16:37:03 +0200 (Tue, 25 Sep 2012) | 3 lines

[...]

[...] Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.

[...]........

[...] r17563 | bugman | 2012-09-25 16:41:25 +0200 (Tue, 25 Sep 2012) | 3 lines

[...]

[...] Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.

[...]........

[...] r17564 | bugman | 2012-09-25 16:42:04 +0200 (Tue, 25 Sep 2012) | 3 lines

[...]

[...] Fix to the Dasha system test needed for the changes to the relax_data.read user function.

[...]........

[...] r17565 | bugman | 2012-09-25 17:02:49 +0200 (Tue, 25 Sep 2012) | 3 lines

[...]

[...] Fix for the Relax_data.test_read unit tests for the relax_data.read user function changes.

[...]........

[...] r17566 | bugman | 2012-09-25 17:07:18 +0200 (Tue, 25 Sep 2012) | 3 lines

[...]

[...] Fix for the Relax_data.test_delete system test for the changes to the relax_data.read user function.

[...]........

[...] r17567 | bugman | 2012-09-25 18:46:03 +0200 (Tue, 25 Sep 2012) | 6 lines

[...]

[...] Fix for bug #20197 (https://gna.org/bugs/?20197) - the PyMOL and Molmol macro failure.

[...]

[...] The macro creation now only operates on spins called 'N' and assumes these are the backbone

[...] nitrogens. The sidechain tryptophan indole NH data will need to be detected and added later.

[...]........

[...] r17568 | bugman | 2012-09-27 10:03:08 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Lots of editing of the model-free GUI section of the user manual.

[...]........

[...] r17569 | bugman | 2012-09-27 10:04:04 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Fix for the comment on the 'Export' button in the BMRB export window.

[...]........

[...] r17570 | bugman | 2012-09-27 10:04:22 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Removed some debugging printouts.

[...]........

[...] r17571 | bugman | 2012-09-27 10:05:14 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Added star versions of the standard spin IDs to the spin ID GUI element (e.g. '@N*', '@H*').

[...]........

[...] r17572 | bugman | 2012-09-27 10:07:03 +0200 (Thu, 27 Sep 2012) | 6 lines

[...]

[...] The CSA setting in the model-free auto GUI analysis now defaults to the '@N*' spin ID.

[...]

[...] Previously no spin ID was being used so that the protons where also having their CSA values set to

[...] that of the nitrogens. Now the execution checking code skips the proton CSA check.

[...]........

[...] r17573 | bugman | 2012-09-27 10:08:12 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the recent test suite data changes.

[...]........

[...] r17574 | bugman | 2012-09-27 16:14:47 +0200 (Thu, 27 Sep 2012) | 6 lines

[...]

[...] Removed the 'force flag' text from the RelaxWarning messages output by the bruker.read user function.

[...]

[...] The force flag arguments of the generic_fns.mol_res_spin.name_spin() and

[...] generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.

[...]........

[...] r17575 | bugman | 2012-09-27 16:29:40 +0200 (Thu, 27 Sep 2012) | 7 lines

[...]

[...] Fix for bug #20201 (https://gna.org/bugs/?20201).

[...]

[...] The bruker.read user function can now handle the situation where multiple spins per residue are

[...] already loaded prior to the user function call. The isotope value from the DC file is now

[...] translated to the element name and this is used as part of the spin ID string.

[...]........

[...] r17576 | bugman | 2012-09-27 19:19:13 +0200 (Thu, 27 Sep 2012) | 3 lines

[...]

[...] Some changes in preparation for Python 3.

[...]........

[...] r17577 | bugman | 2012-09-28 10:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines

[...]

[...] Fix for a fatal bug introduced in the last revision (r17576).

[...]........

[...] r17578 | bugman | 2012-09-28 10:49:08 +0200 (Fri, 28 Sep 2012) | 5 lines

[...]

[...] Removed all of the xrange() calls from the system tests as these are not necessary.

[...]

[...] This is in preparation for Python 3.

[...]........

[...] r17579 | bugman | 2012-09-28 10:55:55 +0200 (Fri, 28 Sep 2012) | 3 lines

[...]

[...] Python 3 preparation - changed the import of SystemTestCase to use the absolute module path.

[...]........

[...] r17580 | bugman | 2012-09-28 10:57:54 +0200 (Fri, 28 Sep 2012) | 3 lines

[...]

[...] Python 3 preparation - the test_suite.system_tests package now uses the absolute module path for imports.

[...]........

[...]

[...]

(Browse SVN revision 17831)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 11:42:50 AM UTC, SVN revision 17552:

Fix for bug #20198 (https://gna.org/bugs/?20198) - the relaxation data back-calculation error.

The problem was that the call to the model-free overfit_deselect() method was deselecting any spins
lacking relaxation data! This should not happen, as no spins need to have relaxation data for this
calculation.

(Browse SVN revision 17552)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 10:20:27 AM UTC, original submission:

This problem is demonstrated by running the script test_suite/shared_data/model_free/sphere/create_ri.py. The issue is at the relax_data.back_calc user function stage where all spins are deselected due to missing relaxation data!

relax> relax_data.back_calc(ri_id='NOE_900', ri_type='NOE', frq=900000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

Over-fit spin deselection.

RelaxWarning: The spin '#sphere_mol1:1@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:1@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:1@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:2@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:2@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:2@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:3@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:3@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:3@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:4@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:4@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:4@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:5@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:5@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:5@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:6@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:6@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:6@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:7@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:7@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:7@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:8@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:8@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:8@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:9@N' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:9@H' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:9@H' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:10@NE1' has been deselected because of missing relaxation data.
RelaxWarning: The spin '#sphere_mol1:10@HE1' has been deselected because of an absence of relaxation mechanisms.
RelaxWarning: The spin '#sphere_mol1:10@HE1' has been deselected because of missing relaxation data.

relax> relax_data.back_calc(ri_id='R1_900', ri_type='R1', frq=900000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

relax> relax_data.back_calc(ri_id='R2_900', ri_type='R2', frq=900000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

relax> relax_data.back_calc(ri_id='NOE_500', ri_type='NOE', frq=500000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

relax> relax_data.back_calc(ri_id='R1_500', ri_type='R1', frq=500000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

relax> relax_data.back_calc(ri_id='R2_500', ri_type='R2', frq=500000000.0)
RelaxWarning: The precise spectrometer frequency should be suppled, a value such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

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

 

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    Date Changed By Updated Field Previous Value => Replaced By
    Tue 25 Sep 2012 11:43:05 AM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
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