bugrelax - Bugs: bug #20197, The PyMOL and Molmol macro...

 
 
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bug #20197: The PyMOL and Molmol macro creation user functions fail when multiple spins per residue are present.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Tue 25 Sep 2012 08:24:49 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 04:46:03 PM UTC, SVN revision 17567:

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.

(Browse SVN revision 17567)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 01:21:44 PM UTC, SVN revision 17561:

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.

(Browse SVN revision 17561)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 01:18:23 PM UTC, SVN revision 17560:

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).

(Browse SVN revision 17560)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 12:05:41 PM UTC, SVN revision 17554:

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.

(Browse SVN revision 17554)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 25 Sep 2012 08:24:49 AM UTC, original submission:

For proteins when analysing both the backbone NH data together with the tryptophane sidechain indole NH data, executing the macro creation user functions:

pymol.macro_apply
pymol.macro_write
molmol.macro_apply
molmol.macro_write

results in the following error:

RelaxError: Only a single spin per residue is allowed for the classic macro style.

This should not occur! Instead the spin types should be automatically detected and handled.

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 04:46:14 PM UTCbugmanStatusNone=>Fixed
      Assigned toNone=>bugman
      Open/ClosedOpen=>Closed
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