bugrelax - Bugs: bug #21591, Hetero NOE calculation fails...

 
 
Show feedback again

bug #21591: Hetero NOE calculation fails (trunk: r22114)

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Tue 04 Feb 2014 02:01:13 PM UTC  
 
Category: relax's source codeSpecific analysis category: Steady state NOE calculation
Priority: 9 - ImmediateSeverity: 5 - Blocker
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 3.1.4Operating System: All systems

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

Tue 04 Feb 2014 03:05:41 PM UTC, SVN revision 22121:

Merged revisions 22117 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22117 | bugman | 2014-02-04 15:46:47 +0100 (Tue, 04 Feb 2014) | 9 lines

Fix for bug #21591 (https://gna.org/bugs/?21591), the complete failure of the NOE analysis.

This bug was reported by Martin Ballaschk (https://gna.org/users/mab).

The issue was introduced in the fix for bug #21562 (https://gna.org/bugs/?21562). The problem is
that the overfit_deselect() method was deselecting all spins with two data points or less rather
than one or less.
........

(Browse SVN revision 22121)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 04 Feb 2014 03:03:48 PM UTC, SVN revision 22119:

Merged revisions 22115 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22115 | bugman | 2014-02-04 15:29:24 +0100 (Tue, 04 Feb 2014) | 9 lines

Created the Noe.test_bug_21591_noe_calculation_fail system test.

This is to catch bug #21591 (https://gna.org/bugs/?21591) submitted by Martin Ballaschk
(https://gna.org/users/mab). This is the complete failure of the NOE analysis.

The peak lists attached to the bug report have been included in the test suite to create the system
test.
........

(Browse SVN revision 22119)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 04 Feb 2014 02:46:47 PM UTC, SVN revision 22117:

Fix for bug #21591 (https://gna.org/bugs/?21591), the complete failure of the NOE analysis.

This bug was reported by Martin Ballaschk (https://gna.org/users/mab).

The issue was introduced in the fix for bug #21562 (https://gna.org/bugs/?21562). The problem is
that the overfit_deselect() method was deselecting all spins with two data points or less rather
than one or less.

(Browse SVN revision 22117)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 04 Feb 2014 02:29:24 PM UTC, SVN revision 22115:

Created the Noe.test_bug_21591_noe_calculation_fail system test.

This is to catch bug #21591 (https://gna.org/bugs/?21591) submitted by Martin Ballaschk
(https://gna.org/users/mab). This is the complete failure of the NOE analysis.

The peak lists attached to the bug report have been included in the test suite to create the system
test.

(Browse SVN revision 22115)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 04 Feb 2014 02:13:38 PM UTC, comment #1:

This bug was probably introduced when fixing bug #21562 (https://gna.org/bugs/?21562) a few days ago.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 04 Feb 2014 02:01:13 PM UTC, original submission:

Hi Edward,

I noticed that the NOE is not calculated anymore in the latest relax version (I just checked out r22114). The noe.out file consists only of "None" values. Relax warns:

relax> calc(verbosity=1)

Over-fit spin deselection:
RelaxWarning: The spin '#XYZ_mol1:120@N' has been deselected because of insufficient data.

But I'm not sure why it deselects every residue and what the criterion is to deselect any residue.

The relax 2.2.4 I keep around in case of an issue with a new release calculates it correctly, my guess is that this is also true for earlier 3.x versions.

I attached a minimal dataset with the standard calculation procedure for calculation of non-replicated spectra with error estimation from baseplane RMSD.

Cheers!

Martin Ballaschk <mab>

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #19958:  noe.test.zip added by mab (4kB - application/zip)

 

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 mab (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 9 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 04 Feb 2014 02:58:11 PM UTCbugmanSpecific analysis categoryNone=>Steady state NOE calculation
    Tue 04 Feb 2014 02:47:52 PM UTCbugmanSeverity3 - Normal=>5 - Blocker
      Priority5 - Normal=>9 - Immediate
      StatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
      ReleaseRepository: trunk=>3.1.4
    Tue 04 Feb 2014 02:12:40 PM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
    Tue 04 Feb 2014 02:01:13 PM UTCmabAttached File-=>Added noe.test.zip, #19958
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup