bugNESSY - Bugs: bug #19834, Unhandled exception during model...

 
 
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bug #19834: Unhandled exception during model fitting

Submitted by:  None
Submitted on:  Fri 22 Jun 2012 06:03:13 PM UTC  
 
Category: NESSY source codeSeverity: 3 - Normal
Priority: 5 - NormalStatus: Postponed
Privacy: PublicAssigned to: Edward d Auvergne <bugman>
Originator Email: -unavailable-Open/Closed: Open

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Tue 26 Jun 2012 04:43:30 PM UTC, comment #2:

Total relaxation time of 0.060 s

CPMG frequencies:
202.020
408.163
618.544
833.333
1052.63
1052.63
1276.65
1505.34
1739.13
1977.85
2222.22

  1. (ref)

Example data points:
3116168
3164902
3157731
3174666
3189502
3223043
3191028
3191554
3206580
3242818
3223700
9847996

Anonymous
Tue 26 Jun 2012 06:44:38 AM UTC, comment #1:

This was first reported in the thread starting at https://mail.gna.org/public/nessy-users/2012-06/msg00000.html.

Dan, could you include the single line that you copied from Excel to NESSY in the report, as well as the nu_CPMG values and the total relaxation period length? If you could give as much information as possible so that I can follow your steps exactly and identically, I should hopefully then be able to reproduce the bug and hunt it down.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri 22 Jun 2012 06:03:13 PM UTC, original submission:

Running Ubuntu 10.04.4 LTS in a VirtualBox VM version 4.1.16. I process and analyze NMR data that is in a VirtualBox Shared Folder.

After launching nessy from the command line, I set the project folder as the directory from which NESSY launched and selected a PDB file from that same directory, then clicked next step.

The Import Peak List and Import Multiple Peak List functions did not work, so as a workaround I copied a single row from an Excel file into the appropriate row in NESSY's data matrix.

I entered the CPMG frequencies and total relaxation delay using the Set up button, set Experiment Type to CPMG Relaxation Dispersion, and Heteronculear Frequency to 60.82, then clicked next step to go to the Analysis tab, and clicked Evaluate Data, which produced this output:

Evaluating Datasets and Experiments:
==================================================
Checking if project folder is set up... [Ok]
Evaluating Experiment 1.....
=============================================
Checking if datasets are set up... [Ok]
Checking if values are entered correctly... [Ok]
Checking if reference spectrum is set up... [Ok]
Experiment 1 checked.
-----------------------------------------------------------------
1 experiment will be analyzed.
-----------------------------------------------------------------

Then I clicked Start Calculation and this output was generated:

Experiment mode: CPMG relaxation dispersion.

------------------------------------------------------
Starting CPMG dispersion curvefit.
------------------------------------------------------

Calculating R2eff...

Calculated R2eff for Residue 8 of Dataset 1 (R2eff = 19.177732348)
Calculated R2eff for Residue 8 of Dataset 2 (R2eff = 18.9190981876)
Calculated R2eff for Residue 8 of Dataset 3 (R2eff = 18.9569041833)
Calculated R2eff for Residue 8 of Dataset 4 (R2eff = 18.8677592125)
Calculated R2eff for Residue 8 of Dataset 5 (R2eff = 18.7900531825)
Calculated R2eff for Residue 8 of Dataset 6 (R2eff = 18.6157006393)
Calculated R2eff for Residue 8 of Dataset 7 (R2eff = 18.7820810129)
Calculated R2eff for Residue 8 of Dataset 8 (R2eff = 18.7793339532)
Calculated R2eff for Residue 8 of Dataset 9 (R2eff = 18.7010505682)
Calculated R2eff for Residue 8 of Dataset 10 (R2eff = 18.5137546306)
Calculated R2eff for Residue 8 of Dataset 11 (R2eff = 18.612303575)

2 repetitions detected at 1.053 Hz

Variance for residue 8 at 1.053 Hz is 0.0151994046602

Pooled variance for residue 8 is 0.0151994046602

Fitting Model 1 to Residue 8

R2o: 15.1
R2o: 15.1
R2o: 15.1
R2o: 15.100
R2o: 16.954
R2o: 16.954
R2o: 17.890
R2o: 17.890
R2o: 18.377
R2o: 18.377
R2o: 18.655
R2o: 18.655
R2o: 18.837
R2o: 18.837
R2o: 18.813
R2o: 18.813
R2o: 18.825
R2o: 18.825
R2o: 18.819
R2o: 18.819
R2o: 18.822
R2o: 18.822
R2o: 18.820
R2o: 18.820
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
R2o: 18.821
NESSY error> Unhandled exception in thread started by
NESSY error>
NESSY error> Traceback (most recent call last):
NESSY error> File "/usr/share/nessy/elements/redirect.py", line 93, in write
NESSY error>
NESSY error> self.report.SetSelection(self.max-self.pageno)
NESSY error> File "/usr/lib/python2.6/dist-packages/wx-2.8-gtk2-unicode/wx/_controls.py", line 3013, in SetSelection
NESSY error>
NESSY error> return controls.BookCtrlBase_SetSelection(*args, **kwargs)
NESSY error> File "/usr/share/nessy/func/calc.py", line 54, in _init_
NESSY error>
NESSY error> CPMG_fit(self.main, self.exp_mode)
NESSY error> File "/usr/share/nessy/curvefit/calc_cpmg_models.py", line 110, in _init_
NESSY error>
NESSY error> self.calculate()
NESSY error> File "/usr/share/nessy/curvefit/calc_cpmg_models.py", line 198, in calculate
NESSY error>
NESSY error> self.model1(self.exp_mode)
NESSY error> File "/usr/share/nessy/curvefit/calc_cpmg_models.py", line 1200, in model1
NESSY error>
NESSY error> self.minimise(i, directory, 0, 1, mode)
NESSY error> File "/usr/share/nessy/curvefit/calc_cpmg_models.py", line 1082, in minimise
NESSY error>
NESSY error> self.plot(model_fit[0], x, y, directory, residue, model, chi2)
NESSY error> File "/usr/share/nessy/curvefit/calc_cpmg_models.py", line 395, in plot
NESSY error>
NESSY error> p.append(model_fit[exp]) # R2
NESSY error> IndexError
NESSY error> :
NESSY error> invalid index to scalar variable.
NESSY error>

(Note: When I tried this with a much more populated matrix of peak heights, not just one residue, the output ended with R2o: 18.821, the terminal displayed "Unhandled exception in thread started by", and the Traceback was not shown.)

Anonymous

 

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    Follow 4 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed 02 Apr 2014 12:39:41 PM UTCbugmanStatusIn Progress=>Postponed
    Tue 26 Jun 2012 06:46:02 AM UTCbugmanAssigned toNone=>bugman
    Tue 26 Jun 2012 06:45:56 AM UTCbugmanCategoryNone=>NESSY source code
    Tue 26 Jun 2012 06:44:38 AM UTCbugmanStatusNone=>In Progress
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