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Subject:

Not exactly a bug, but...

From:

Dr Horst Schirra <[log in to unmask]>

Reply-To:

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

Date:

Wed, 23 Apr 2008 16:23:51 +1000

Content-Type:

multipart/mixed

Parts/Attachments:

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text/plain (33 lines) Parts/Attachments

multipart/mixed (33 lines) , text/plain (83 lines)

...possibly not a feature either:

I did recently create a molecular system containing a cyclic peptide
(with the N- and C-terminus connected by a peptide bond).

When I enter the peptide sequence in the form ACDEFGH... and tick the
box for "cyclic peptide", the resulting chain is starting with amino
acid 2, i.e. I get the sequence A2-C3-D4-E5... instead of A1-C2-D3-E4... 

Is that behaviour intended by analysis? 

It's not a problem, as it can easily be corrected by setting the "chain
starts with amino acid number" to 0. But it would be nice if it either
came out correct without having to do that, or if there was a note in
the manual/tutorial/help pages that one has to set the starting number
to zero for cyclic proteins - so that people don't have to do the chain
creation twice, because the first time didn't give the intended result. :)

Cheers,

Horst Joachim Schirra

     ----------------------------------------------------------------
    / Dr. sc. nat. Horst Joachim Schirra    Phone: (+61)7/3346-2021 /
   / Queensland Smart State Fellow          Fax:  (+61)7/3346-2101 /
  / Institute for Molecular Bioscience                            /
 / University of Queensland           email: [log in to unmask] /
/ Brisbane QLD 4072, Australia   http://www.uq.edu.au/~uqhschir /
----------------------------------------------------------------





Hi Wayne, >But anyway, on the real point at hand, it sounds like indeed we ought to >have functionality to remove points from a condition series. (I think >it's grayed out now in this specific case but it should be possible to >allow it. I'll discuss with Tim.) This would be great and exactly what would be needed to import Bruker relaxation data directly into Analysis. As it turns out deleting the peaks for the blank planes only worked in about 70% of cases, for some I still get the zero points included in the graph (see fig) but if I click "remove point" to remove the zeros I get >>> Exception in Tkinter callback Traceback (most recent call last):   File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__     return self.func(*args)   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/EditFitGraphPopup.py", line 306, in removePoint     self.object.delete()   File "/data/prog/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py", line 294, in delete ApiError: ccp.nmr.Nmr.Peak.delete:called on deleted object:    It seems I am also still having a bit of trouble with this pseudo3d data collected with the time series in the second dimension. The copy peak assignments gives me errors like >>> Exception in Tkinter callback Traceback (most recent call last):   File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__     return self.func(*args)   File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 456, in callit     func(*args)   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/CopyPeakAssignmentsPopup.py", line 458, in update     dimMapping = self.getDimMapping()   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/CopyPeakAssignmentsPopup.py", line 299, in getDimMapping     mapping2 = getDataDimAxisMapping(self.targetPeakList.dataSource, window)   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/WindowBasic.py", line 1485, in getDataDimAxisMapping     if dataDim.findFirstDataDimRef().expDimRef.isotopeCodes == isotopes: AttributeError: 'SampledDataDim' object has no attribute 'findFirstDataDimRef' and if I try and copy from assignments from a HSQC onto the HSQC plane of the series then I get a "No Peaks in source table" pop up. Also using "propogate assignments" works on some peaks but on others it cannot propogate the assignment of the Nitrogen resoanance and when I try and assign it manually I get the error >>> Exception in Tkinter callback Traceback (most recent call last):   File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__     return self.func(*args)   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/EditAssignmentPopup.py", line 157, in <lambda>     command=lambda n=i:self.newResonance(n),   File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/EditAssignmentPopup.py", line 268, in newResonance     resonance = newResonance(project, isotopeCode=self.peakDim.dataDimRef.expDimRef.isotopeCodes[0]) AttributeError: 'NoneType' object has no attribute 'expDimRef'    For 70% of the peaks tho, the rate analysis using the pseudo3d with the time series in the 2nd dimension works perfectly! Cheers Ben

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