bugrelax - Bugs: bug #21562, NOE analysis issue - failure to...

 
 
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bug #21562: NOE analysis issue - failure to calculate the NOE when both the saturated and reference spectra are replicated.

Submitted by:  Dhanas Muthu <dhanas>
Submitted on:  Thu 30 Jan 2014 05:14:31 PM UTC  
 
Category: relax's source codeSpecific analysis category: Steady state NOE calculation
Priority: 5 - NormalSeverity: 4 - Important
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 3.1.3Operating System: All systems

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

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 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.
Fri 31 Jan 2014 09:43:43 AM UTC, SVN revision 22089:

Merged revisions 22088 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22088 | bugman | 2014-01-31 10:42:52 +0100 (Fri, 31 Jan 2014) | 10 lines

Fix for bug #21562, the failure of the NOE analysis when spectra are replicated.

This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu (https://gna.org/users/dhanas).

The problem was that the NOE overfit_deselect() method was deselecting all spins which do not have
exactly 2 intensity values. This is incompatible with replicated spectra as the number will be
greater than two. The check has been modified to deselect spins only when the number of intensity
values are zero or one (i.e. < 2 rather than != 2).
........

(Browse SVN revision 22089)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 09:42:52 AM UTC, SVN revision 22088:

Fix for bug #21562, the failure of the NOE analysis when spectra are replicated.

This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu (https://gna.org/users/dhanas).

The problem was that the NOE overfit_deselect() method was deselecting all spins which do not have
exactly 2 intensity values. This is incompatible with replicated spectra as the number will be
greater than two. The check has been modified to deselect spins only when the number of intensity
values are zero or one (i.e. < 2 rather than != 2).

(Browse SVN revision 22088)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 09:37:40 AM UTC, SVN revision 22086:

Merged revisions 22083 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22083 | bugman | 2014-01-31 10:36:17 +0100 (Fri, 31 Jan 2014) | 10 lines

Created the Noe.test_bug_21562_noe_replicate_fail system test.

This is to catch bug #21562 (https://gna.org/bugs/?21562), reported by Dhanas Muthu
(https://gna.org/users/dhanas). This is the failure of the NOE analysis when spectra are
replicated.

This uses the truncated data taken from the files attached to the bug report. The NOE output file
is checked to see if the contents are correct.
........

(Browse SVN revision 22086)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 09:36:17 AM UTC, SVN revision 22083:

Created the Noe.test_bug_21562_noe_replicate_fail system test.

This is to catch bug #21562 (https://gna.org/bugs/?21562), reported by Dhanas Muthu
(https://gna.org/users/dhanas). This is the failure of the NOE analysis when spectra are
replicated.

This uses the truncated data taken from the files attached to the bug report. The NOE output file
is checked to see if the contents are correct.

(Browse SVN revision 22083)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 09:05:03 AM UTC, comment #3:

For reference, this problem was first reported on the relax users mailing list at http://thread.gmane.org/gmane.science.nmr.relax.user/1543.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 08:51:00 AM UTC, SVN revision 22081:

Merged revisions 22080 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22080 | bugman | 2014-01-31 09:50:28 +0100 (Fri, 31 Jan 2014) | 9 lines

Added the truncated data for creating a system test to catch bug #21562.

This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu (https://gna.org/users/dhanas)
and is the failure of the NOE analysis when spectra are replicated.

This consists of the Sparky peak lists attached to the bug report and the modified 2AT7 PDB file.
The data has been truncated to only include residues :12, :13, and :14.
........

(Browse SVN revision 22081)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 31 Jan 2014 08:50:30 AM UTC, SVN revision 22080:

Added the truncated data for creating a system test to catch bug #21562.

This bug (https://gna.org/bugs/?21562) was reported by Dhanas Muthu (https://gna.org/users/dhanas)
and is the failure of the NOE analysis when spectra are replicated.

This consists of the Sparky peak lists attached to the bug report and the modified 2AT7 PDB file.
The data has been truncated to only include residues :12, :13, and :14.

(Browse SVN revision 22080)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 30 Jan 2014 05:14:31 PM UTC, original submission:

Hi Edward,

I have trouble analyzing NOE data using duplicate spectra for error estimation. It works just fine if I use only one set of data (one reference and one saturated) and baseplane rmsd for error calculation. Also no problems for R1 and R2 calculations even if I use many replicated spectra for error calculations.

I just used the default parameters of relax for this calculation. My procedure:
1) set the working directory
2)load the spin system (used modified pdb file, worked fine for R1 and R2 calculation)
3)load the sparky list files (zip file containing those files attached for your use)
4) execute the run using default values

The calculation creates a .out file with NOE and error values as null.

Hope you can figure this! Or I may be doing something wrong.

Thanks for your help.

Dhanas

Dhanas Muthu <dhanas>

 

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Attach File(s):
   
   
Comment:
   

Attached Files
file #19920:  noe-error-message.txt added by bugman (49kB - text/plain - This is the relax log messages from the RTF file attached to http://thread.gmane.org/gmane.science.nmr.relax.user/1543.)
file #19906:  Sparky_peaklist.zip added by dhanas (8kB - application/zip)
file #19907:  2AT7_fmf.pdb added by dhanas (223kB - application/octet-stream)
file #19908:  noe.600.out added by dhanas (15kB - 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 dhanas (Submitted the item)
  • -unavailable- added by dhanas
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    Follow 14 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 04 Feb 2014 02:58:31 PM UTCbugmanSpecific analysis categoryNone=>Steady state NOE calculation
    Fri 31 Jan 2014 09:44:11 AM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Fri 31 Jan 2014 08:45:57 AM UTCbugmanCategoryNone=>relax's source code
    Fri 31 Jan 2014 08:45:48 AM UTCbugmanOperating SystemMac OS X (Intel)=>All systems
    Fri 31 Jan 2014 08:37:49 AM UTCbugmanAttached File-=>Added noe-error-message.txt, #19920
    Fri 31 Jan 2014 08:22:02 AM UTCbugmanSummaryNOE analysis issue=>NOE analysis issue - failure to calculate the NOE when both the saturated and reference spectra are replicated.
    Fri 31 Jan 2014 08:21:31 AM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
    Fri 31 Jan 2014 08:13:02 AM UTCbugmanPrivacyPrivate=>Public
    Thu 30 Jan 2014 05:14:31 PM UTCdhanasAttached File-=>Added Sparky_peaklist.zip, #19906
      Attached File-=>Added 2AT7_fmf.pdb, #19907
      Attached File-=>Added noe.600.out, #19908
      Carbon-Copy-=>Added dhanas
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