Dear Ben,
We can only get so far with this one. What seems to be happening is that
the information in your MolSystem.xml file is out of synch with the
information in your top level project.xml file. There is a structure
obiject that should be linked to a ContentStorage object with serial 65,
but there is no such ContenetStorage object around.
We would have to look at the data to get any further, but even that might
not be enough. The MolSystem file corresponds to a structure being
present but the project file corresponds to it not being present. The most
likely explanations are:
1) at some point you exited having backed up some, but not all, changed
files.
2) There was an error that aborted the backup in the middle.
3) There is a bug in either the PDB load code or the deletion code that
leaves the project in an incorrect state.
Could you send all the xml fiels relevant to teh project,m for us to look
at?
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, 4 Sep 2006, [ISO-8859-1] Ben Goult wrote:
> Hi
>
> I have just successfully read in the cyana outputted pdb files into my
> analysis project, I saved the project and all was good.
>
> Then I looked and I had read in the file twice so I actually had 40
> structures in my project (2x20). This isnt a major problem as I can just
> delete them using Structure:Edit Structure.
>
> However, I tried to load my backup project file and it failed. I got the
> following traceback:
>
> ERROR loading xml ccpnmr.Analysis ccpnmr/Analysis.xml
> 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/memops/gui/ScrolledMatrix.py",
> line 571, in mouseDoubleClick
> self.selectDoubleCell(row,col)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/ScrolledMatrix.py",
> line 546, in selectDoubleCell
> self.doubleCallback(self.currentObject, objRow, objCol)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/FileSelect.py", line
> 395, in doubleCallback
> self.double_callback(file)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/BasePopup.py", line
> 224, in ok
> if (not self.apply()):
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/editor/OpenProjectPopup.py", line
> 142, in apply
> self.callback(self.project)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 911, in initProject
> Analysis.initProject(self, project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
> line 194, in initProject
> self.checkAxisPanels()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
> line 139, in checkAxisPanels
> for window in self.project.spectrumWindows:
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 18612, in getSpectrumWindows
> otherStorage.load()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 8904, in load
> ioModule.load(stream, self.project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/xml/Analysis.py", line
> 108, in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 370, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 532, in doLoad
> loadDelayedData(objectDict, delayedLoadData)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 1016, in loadDelayedData
> target = getByKey(clazz,fullKey)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/general/Implementation.py", line
> 289, in getByKey
> value = current.__dict__[downlinks[ii]] or getattr(current,downlinks[ii])
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 11115, in getChemCompHeads
> otherStorage.load()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 8904, in load
> ioModule.load(stream, self.project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccp/xml/Molecule.py", line 102,
> in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 374, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 546, in doLoad
> fileVersion, result)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/Compatibility.py",
> line 111, in postProcess
> return process (packageName, fromVersion, headObject, dataConverters)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/Compatibility.py",
> line 186, in process
> target = func(target)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/Compatibility.py",
> line 933, in conv_ccp_Molecule_1_0_208
> if (molecule.chains
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccp/api/Molecule.py", line 7179,
> in getChains
> otherStorage.load()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 8904, in load
> ioModule.load(stream, self.project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccp/xml/MolSystem.py", line 101,
> in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 374, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py", line
> 657, in doLoad
> raise ApiError(
> ApiError: Error loading fileNo ContentStorage object found from key:
> [65]
>
> This is not a major problem here as I can easily delete the structures
> manually but I would not want this to happen after I had saved something
> unwanted into my project.
>
> Is it because I have added new coordinates into my project which the old
> project is not expecting?
>
> Cheers
>
> Ben
>
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