Hi Tim,
Looks great, thank you. I can now run Nexus on my protein with a phosphoserine.
However, I am now having trouble exporting a peaklist for input into
MARS. This seems to be independent of the modified residue from
before. Here is the error message:
Exception in Tkinter callback
Traceback (most recent call last):
File "/Applications/ccpnmr2/python2.6/lib/python2.6/lib-tk/Tkinter.py",
line 1410, in __call__
return self.func(*args)
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py",
line 565, in <lambda>
self.exportButton[component] = Tkinter.Button(master, text =
"Export %s file." % component, command = lambda comp = component:
self.importExportFile(comp))
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py",
line 799, in importExportFile
returnValue = rwFunc(*addArgs,**addKeywds)
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py",
line 985, in writeProject
returnValue = self.createFullProject(fileName,**keywds)
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/MarsFormat.py",
line 194, in createFullProject
self.writeShifts(os.path.join(self.inputDirectory,chemShiftFile),
measurementList = self.shiftList, chains = [self.chain],
ignoreFixedConnection = ignoreFixedConnection, noWrite = True,
minimalPrompts = self.minimalPrompts)
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py",
line 2055, in writeShifts
return self.writeMeasurements(*args, **keywds)
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py",
line 2164, in writeMeasurements
self.setMeasurementFileValues()
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py",
line 9818, in setMeasurementFileValues
self.setSpecificSpinSystemInfo()
File "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/format/converters/MarsFormat.py",
line 378, in setSpecificSpinSystemInfo
if prevResonanceToSpinSystem and (self.ignoreFixedConnection or
(not resonanceToSpinSystem.linkedSpinSystems.has_key(1) and not
prevResonanceToSpinSystem.linkedSpinSystems.has_key(-1))):
AttributeError: 'NoneType' object has no attribute 'linkedSpinSystems'
Any ideas?
Thanks again, and I hope that is all for now.
~Jeremy
On Tue, Aug 24, 2010 at 8:07 AM, Wayne Boucher <[log in to unmask]> wrote:
> Hello,
>
> Tim has changed the code (in a more subtle way than the change I proposed)
> so hopefully it should work on the phosphoserine variant as well now.
>
> Wayne
>
> On Mon, 23 Aug 2010, Jeremy wrote:
>
>> Hi Wayne,
>>
>> Thanks for the quick reply. I created a new molecule, one with a
>> regular serine, and Nexus now works well. So, that does appear to be
>> the problem.
>>
>> Thanks again,
>> Jeremy
>>
>>
>> On Mon, Aug 23, 2010 at 2:56 PM, Wayne Boucher <[log in to unmask]>
>> wrote:
>>>
>>> Hello,
>>>
>>> I have looked at the code and can see where it is likely to be going
>>> wrong
>>> and it would indeed be because of phosphoserine. I could change the code
>>> but I'll have to ask Tim (currently in Australia) if the change is ok.
>>>
>>> Wayne
>>>
>>> On Mon, 23 Aug 2010, Jeremy wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am using CCPN to auto-assign a protein for which I have manually
>>>> picked peaks. I have HNCA, HNCOCA, HNCACB, CBCACONH, and 15N HSQC
>>>> spectra. I have curated a nice list of peaks and followed the
>>>> included instructions closely.
>>>>
>>>> However, when I run Nexus, I get the "Preparing Spin System Typing"
>>>> progress bar stuck at zero. Then, I get the following error:
>>>>
>>>>
>>>> Exception in Tkinter callback
>>>> Traceback (most recent call last):
>>>> File "/Applications/ccpnmr2/python2.6/lib/python2.6/lib-tk/Tkinter.py",
>>>> line 1410, in __call__
>>>> return self.func(*args)
>>>> File
>>>>
>>>> "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/nexus/AutoBackbonePopup.py",
>>>> line 1297, in runNexus
>>>> keepExisting, progressBar)
>>>> File
>>>>
>>>> "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/nexus/AutoBackboneNexus.py",
>>>> line 132, in autoBackboneNexus
>>>> progressBar)
>>>> File
>>>>
>>>> "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/nexus/AutoBackboneNexus.py",
>>>> line 497, in getInitialAssignMatrix
>>>> scores = getShiftsChainProbabilities(shifts, chain)
>>>> File
>>>>
>>>> "/Applications/ccpnmr2/ccpnmr2.1/python/ccpnmr/analysis/core/ChemicalShiftBasic.py",
>>>> line 232, in getShiftsChainProbabilities
>>>> total = sum(probDict.values())
>>>> TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'
>>>>
>>>>
>>>> Nexus works with another, old dataset, so I suspect it is specific to
>>>> the current project. Any ideas what could be the matter? I do have a
>>>> phosphoserine residue in the sequence, could this be the issue?
>>>>
>>>> Thank you in advance for your help!
>>>>
>>>> ~Jeremy
>>>>
>>>
>
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