Hello Dr Wayne,
I have now just seen your reply. I was not complaining about the warning that
two peaks not having heights.
I have four glycines in the sequence (all of which have assigned peaks in the
HNHA spectrum). But when I check the option asking the glycines to be shown, I
see only one of the glycines in the table. Coupling values for remaining three
are still not showing up.
It could be some mistake from my side which I am not able to figure out. The 3J
HnHa values for the remaining three glycines are not very critical as I can get
the predictions for dihedral angles via DANGLE and/or TALOS+. However, I wanted
to know where the error is.
with regards,
Aswani
> Hello,
>
> Ok, that is a graphical interface "chicken and egg" problem. There is a
> warning, but the "parent" widget is not ready yet, so when the warning dialog is
> popped up, Tk throws a wobbly. I've protected against that now (patch on the
> update server).
>
> The warning was just that two of the peaks don't have heights. It's a bit
> irritating having that message continually pop up so possibly it should just
> print that warning to the screen.
>
> Wayne
>
> On 8 Sep 2014, at 15:08, Aswani Kumar Kancherla wrote:
>
>> Hello Dr Wayne,
>>
>> Many thanks for the prompt reply.
>>
>> I have upgraded the Analysis to version 2.4.0. I could open the project
>> without
>> any hassle but the error (or a similar one) seems to still exist when I try to
>> extarct 3J HN-HA values. I am attaching the traceback below.
>>
>> with regards,
>> Aswani Kumar
>>
>> traceback in Analysi version 2.4.0
>> ===============================================================================================================================
>> Exception in Tkinter callback
>> Traceback (most recent call last):
>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
>> 1410, in __call__
>> return self.func(*args)
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/AnalysisPopup.py",
>> line 2214, in calcHnHaCoupling
>> self.openPopup('calc_hnha_coupling', CalcHnHaCouplingPopup)
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/AnalysisPopup.py",
>> line 1805, in openPopup
>> transient=transient, *args, **kw)
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>> line 187, in __init__
>> BasePopup.__init__(self, parent=parent, title=u'Data Analysis : 3J
>> H-H\u03B1
>> Coupling', **kw)
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/popups/BasePopup.py",
>> line 89, in __init__
>> memops.editor.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
>> File "/home/nmrware/ccpnmr/ccpnmr2.4/python/memops/editor/BasePopup.py", line
>> 85, in __init__
>> memops.gui.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
>> File "/home/nmrware/ccpnmr/ccpnmr2.4/python/memops/gui/BasePopup.py", line
>> 128, in __init__
>> self.initial_focus = self.body(frame)
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>> line 398, in body
>> self.updateKarplusCurve()
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>> line 447, in updateKarplusCurve
>> self.couplingData = couplingData = self.extractHnHaCouplingData()
>> File
>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>> line 1320, in extractHnHaCouplingData
>> parent=self)
>> File "/home/nmrware/ccpnmr/ccpnmr2.4/python/memops/gui/MessageReporter.py",
>> line 87, in showWarning
>> return tkMessageBox.showwarning(title, message, parent=parent)
>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/tkMessageBox.py",
>> line 85, in showwarning
>> return _show(title, message, WARNING, OK, **options)
>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/tkMessageBox.py",
>> line 72, in _show
>> res = Message(**options).show()
>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/tkCommonDialog.py",
>> line 48, in show
>> s = w.tk.call(self.command, *w._options(self.options))
>> TclError: bad window path name ".47007760.1131085456.__tk__messagebox"
>>
>> ============================================================================================================================================
>>
>>> Hello,
>>>
>>> That was a bug which I think was fixed in Analysis 2.2 so if you can upgrade
>>> (the latest is 2.4.0 but we'll have a 2.4.1 soonish) that would be ideal.
>>> The
>>> problem with the code (as it was) is that it only worked for "standard" amino
>>> acids (well, and for some reason also 'Cyss') and "standard" atoms. For Gly
>>> it
>>> is looking for one of C, CA, H, HA2, HA3 or N. Unfortunately the way the
>>> code
>>> was written it seems to have been looking for HA in the spot where it fell
>>> over
>>> for you (the way I understand it).
>>>
>>> Wayne
>>>
>>> On 8 Sep 2014, at 12:53, Aswani Kumar wrote:
>>>
>>>> Hello Analysis Users,
>>>>
>>>> I am getting an error and the following trace back when I select the "show
>>>> glycines" option in the pop-up M :: DataAnalysis :: 3J-H-Ha-coupling for
>>>> extracting J coupling values from a 3D-HNHA spectrum. However, I am able to
>>>> get the coupling values for other residues. What could be the reason for
>>>> this?
>>>>
>>>> traceback:
>>>> ===============================================================================================================
>>>>
>>>>>>> Exception in Tkinter callback
>>>> Traceback (most recent call last):
>>>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
>>>> 1410, in __call__
>>>> return self.func(*args)
>>>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
>>>> 495, in callit
>>>> func(*args)
>>>> File
>>>> "/home/nmrware/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>>>> line 933, in update
>>>> self.couplingData = couplingData = self.extractHnHaCouplingData()
>>>> File
>>>> "/home/nmrware/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py",
>>>> line 1192, in extractHnHaCouplingData
>>>> score = intensity * getAtomProbability(ccpCode, atomName, ppm)
>>>> TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'
>>>> ================================================================================================================
>>>>
>>>> I am using CcpNmr Analysis version 2.1 (Release 5) on Linux SuSe 11.4 .
>>>>
>>>> thanking you in advance,
>>>>
>>>> K. Aswani Kumar
>>>> Graduate Student
>>>> Molecular Biophysics Unit
>>>> Indian Institute of Science
>>>> Bangalore-560012
>>>> India
>>>
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>>>
>>
>>
>>
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