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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