Dear Marc,
This sounds like the right approach. Also thanks for trying yourself first
before of passing it on to us. I do not expect further trouble - of course
there might be some information missing. Have a look at which other
Resonances your Resonance is bound to and compare it with what you would
expect.
This should not have happened. Given that it has, there seems to be three
likely reasons for the error.
1) One or more _IDREF do not correspond to any _ID in the file. If so just
delete those _IDREF and there will be no further problems.
2) there is an _IDREF that points to the same resonance that contains it.
If so remove that _IDREF and the rest should be OK.
3) One or more _IDREF correspond to _ID that are not Resonances (less
likely). If so just delete those _IDREF and there will be no further
problems.
It would be very strange if the _IDREF that give problems correspond to
the _ID of existing resonances. But you should still be OK. Out of
curiosity you might check if the resonances pointed to have an _IDREF back
to the Resonance that give the error. If yes, the link will be set anyway,
just from the other side. If no the link will disappear. In either case I
really do not understand how this happened.
For your information, the _IDREF refer to the _ID of objects. One-to-one
and many-to-many links are stored on (and set from) both sides.
One-to-many links are stored on (and set from) both sides in older
version, but ony on one side in newer ones. A Resonance may not be
covalently bound to itself, but that did slip b in some old files.
If you find out anything more, could you send it to me, just for
curiosity?
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 Mon, 7 Apr 2008, Marc Lenoir wrote:
> Dear all,
>
> I had the following error when I wanted to restart my project (below). I
> searched the resonance associated with the serial=1082 and I commented out
> all but one "covalentlyBound _IDREF" statements for this resonance in the
> Nmr.xml file. It now works, however, I wanted to know if this is the right
> way of fixing my problem and if my manipulation could cause further problems.
> In particular, I am concerned by the IDREF that are now commented out.
> Should I, for example, check the residues associated with these numbers?
>
> Thanks,
>
> Marc
>
>
> POP-UP:
> -------
>
> Project invalid, please quit, fix and
> re-start:ccp.nmr.Nmr.Resonace.setCovalentlyBound:value cannot be None:
>
> CONSOLE:
> -------
>
> Error dereferencing covalentlyBound for object ccp.nmr.Nmr.Resonance with
> (partial) key :
> ['PROT', 1082]
>
> last xml element read:
> </_StorageUnit>
>
>
> parser state was:
> setting links and multiattributes
>
> ERROR loading xml ccp.nmr.Nmr ccp/nmr/Nmr.xml
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/prog/ccpnmr/python2.4/lib/python2.4/lib-tk/Tkinter.py", line 1345,
> in __call__
> return self.func(*args)
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/gui/BasePopup.py", line 227, in ok
> if (not self.apply()):
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/editor/OpenProjectPopup.py",
> line 142, in apply
> self.callback(self.project)
> File "/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py",
> line 929, in initProject
> Analysis.initProject(self, project)
> File "/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py", line
> 405, in initProject
> self.initTopObjects(project)
> File "/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py", line
> 195, in initTopObjects
> if not project.currentNmrProject:
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py", line
> 18782, in getCurrentNmrProject
> result = self.findFirstNmrProject()
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py", line
> 13173, in findFirstNmrProject
> otherStorage.load()
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py", line
> 9066, in load
> ioModule.load(stream, self.project)
> File "/prog/ccpnmr/ccpnmr1.0/python/ccp/xml/nmr/Nmr.py", line 114, in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line 425,
> in load
> result = doLoad(stream, mapping, headObject)
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line 614,
> in doLoad
> loadDelayedData(objectDict, delayedLoadData)
> File "/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 1042, in loadDelayedData
> setattr(obj,name,targets)
> File "/prog/ccpnmr/ccpnmr1.0/python/ccp/api/nmr/Nmr.py", line 91845, in
> setCovalentlyBound
> raise ApiError("%s.setCovalentlyBound:" % self.qualifiedName +
> ApiError: ccp.nmr.Nmr.Resonance.setCovalentlyBound:value cannot be None:
>
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