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CCPNMR  May 2008

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Subject:

Re: Error with FollowShiftChanges

From:

Kaare Teilum <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Wed, 14 May 2008 15:08:05 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (97 lines)

Hi Rasmus and Tim

Thanks for the fix - it partly works now.

When I in the Follow Shift Changes choose Fit function: Ax + B and click
Group Peaks I get the following warning:

Problem with fitting: method = 1, nIter = 1000, noise = 0.1, x = [], y =
[0.0], xW = [], yW = []: x any y must both be of size 0

After having clicked through a warning for each peak group it is now
possible to export a shift list that appears to be OK. How analysis has
chosen which peaks to group is a mystery to me...

If I instead choose Fit function 'None' I get the following error:

Exception in Tkinter callback
Traceback (most recent call last):
  File "/sw/lib/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
    return self.func(*args)
  File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/FollowShiftChangesPopup.py",
line 873, in groupPeaks
    bestScore = getAlignScore(bestRoute)
  File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/FollowShiftChangesPopup.py",
line 647, in getAlignScore
    fitError = dataFitting.fitError
AttributeError: 'NoneType' object has no attribute 'fitError'


Is the fit function 'None' supposed to mean that peaks will be grouped
according to manually assigned peak lists at each experimental condition?


Thanks for your time,
Kaare


On Wed, 14 May 2008 14:09:37 +0100, Rasmus Fogh <[log in to unmask]>
wrote:

>Dear Kaare,
>
>Tim has fixed the problem, and the fix is on the update server. The
>problem was that there were unassigned peak groups. This export will
>only work if a spin system is present in the peaks group that the shifts
>are followed for.
>
>A "None" spin system could be from lots of separate peak trajectories...
>
>In the future the program will ignore unassigned peak groups rathre than
>throw an error.
>
>Yours,
>
>Rasmus
>
>---------------------------------------------------------------------------
>Dr. Rasmus H. Fogh                  Email: [log in to unmask]
>Dept. of Biochemistry, University of Cambridge,
>80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002
>
>On Wed, 14 May 2008, Kaare Teilum wrote:
>
>> Hi
>>
>> I'm trying to use 'Export Shifts' in the Follow Shift Changes pop-up. When I
>> press the bottom I get the following error:
>>
>> >>> Exception in Tkinter callback
>> Traceback (most recent call last):
>>   File "/sw/lib/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
>>     return self.func(*args)
>>   File
>>
"/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/FollowShiftChangesPopup.py",
>> line 419, in exportShifts
>>     lines = exportSeriesShifts(self.expSeries)
>>   File
>>
"/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/FollowShiftChangesPopup.py",
>> line 154, in exportSeriesShifts
>>     if ss.residue:
>> AttributeError: 'NoneType' object has no attribute 'residue'
>>
>> It seems to me that for some spin-system the residue information is lost or
>> something like that. I'm working with a series of 39 spectra from a pH
>> titration, so it would be really nice to know exactly what to look for as I
>> have both 39 peak lists and 39 shift lists.
>> (I did test the export when I had only around 10 spectra in my serie and it
>> worked then).
>>
>> Cheers,
>> Kaare
>>

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