bugrelax - Bugs: bug #20201, run mf_multimodel.py in relax (cmd)

 
 
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bug #20201: run mf_multimodel.py in relax (cmd)

Submitted by:  None
Submitted on:  Wed 26 Sep 2012 05:21:38 PM UTC  
 
Category: relax sample scriptsSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Mengjun XueOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 2.1.1
Operating 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.
Thu 27 Sep 2012 02:33:38 PM UTC, comment #4:

This problem is two-fold. Firstly relax was expecting only a single spin per residue to be loaded prior to the bruker.read user function call. This behaviour has now changed. Secondly the attached script is problematic. There are two incompatible user function calls in the script:

structure.load_spins('@H', ave_pos=True)

and:

sequence.attach_protons()

Attaching protons where protons already exist does not make sense, and relax naturally quits with the message:

RelaxError: The unnumbered spin name 'H' already exists.

Removing one of the two calls allows the script to run.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 27 Sep 2012 02:29:40 PM UTC, SVN revision 17575:

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.

(Browse SVN revision 17575)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 27 Sep 2012 02:03:56 PM UTC, comment #2:

The 1UBQ_H.PDB file can be downloaded from https://gna.org/bugs/download.php?file_id=16482 (this is attached to bug #20152).

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 27 Sep 2012 01:59:43 PM UTC, comment #1:

The wrong PDB file is attached. The attached file has no protons! The 1UBQ_H.PDB is needed instead.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 26 Sep 2012 05:21:38 PM UTC, original submission:

Dear Dr. Edward d'Auvergne,

Thank you very much for your email. As you suggested, when I editted the py
file in MS wordpad, the problem is solved, but calulation still stopped
somewhere. Attachment please find the py file and the log file. Thank you
very much.

The link https://gna.org/bugs/?20175 is the old bug reports of run mf_multimodel.py in relax (cmd)

With best regards,

Mengjun Xue

Anonymous

 

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Attached Files
file #16606:  log added by None (48kB - text/plain)
file #16607:  mf_multimodel.py added by None (4kB - application/octet-stream)
file #16608:  PDB,NOE,T1,T2.rar added by None (56kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -unavailable- added by None (Submitted the item)
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    Follow 12 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 27 Sep 2012 02:33:48 PM UTCbugmanOriginator Name=>Mengjun Xue
    Thu 27 Sep 2012 02:33:38 PM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
      Release2.1.0=>2.1.1
      Operating SystemMicrosoft Windows=>All systems
    Thu 27 Sep 2012 02:04:49 PM UTCbugmanStatusIn Progress=>Confirmed
    Thu 27 Sep 2012 02:03:56 PM UTCbugmanStatusNeed Info=>In Progress
    Thu 27 Sep 2012 01:59:43 PM UTCbugmanStatusNone=>Need Info
      Assigned toNone=>bugman
    Wed 26 Sep 2012 05:21:38 PM UTCNoneAttached File-=>Added log, #16606
      Attached File-=>Added mf_multimodel.py, #16607
      Attached File-=>Added PDB,NOE,T1,T2.rar, #16608
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