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Hi Wayne, In the [backup]/ccp/molecule, there is no Molecule directory, only the MolSystem directory. I had hoped that by copying over the Molecule directory from the original project directory that it would solve the issue, but the same error messages still appear. I don't know if this is of any use, but I have attached the output of a "diff -r [project] [project_backup]". Best wishes, Pryank Wayne Boucher wrote: > Hello, > > I've had a quick chat with Rasmus and we don't know what has gone wrong. > So it is loading a chain in a MolSystem (specifically chain A of molSystem > MS1) and each such chain points to a molecule. Now the molecule it is > looking for has the (arcane) key AGR2_pryank_2009_03_26-10-44-01-852_00001 > (unfortunately the error message does not give the name of the molecule > but presumably you know what chain A's molecule ought to be). > > What files do you see in the directory ccp/molecule/Molecule? There is > supposed to be one ending with that horrid key above (+ (.xml"). The file > is actually prefixed with the molecule name (with underscores replacing > spaces). Look in both the backup directory and the original project > directory because I guess it's possible that the molecule file (for some > reason) is only in the original directory. (Which would tend to indicate > that the backup failed in its job.) > > Wayne > > On Fri, 17 Apr 2009, Dr. Pryank Patel wrote: > > >> Hi Wayne, >> Thanks for the information. I have tried to open a backup project before but >> failed, which is why I asked, to see where I went wrong. I tried to open the >> backup project from the Open Project dialog, and received a "Project invalid" >> box error message, saying "Project invalid, please quit, fix and restart: >> Linked-to object with ID not found: <ccp.molecule.MolSystem.Chain['MS1', >> 'A']>:molecule:AGR2_pryank_2009_03_26-10-44-01-852_00001". The error message >> in the console is as follows: >> >> >>>>> Error during Exo link dereferencing. Object was: >>>>> >> <ccp.molecule.MolSystem.Chain ['MS1', 'A']> >> values were: ['AGR2_pryank_2009-03-26-10-44-01-852_00001'] >> tag name was: molecule >> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS1']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml', >> mode 'r' at 0x59f2580> >> Last xml tag read: _StorageUnit >> Parser state was: postprocessing data >> Object stack was empty >> Error loading file for: <ccp.nmr.Nmr.NmrProject ['AGR2']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml', >> mode 'r' at 0x59f24f8> >> Last xml tag read: NMR.AtomSet.atoms >> Parser state was: reading >> Current object was: <ccp.nmr.Nmr.AtomSet ['AGR2', 1]> >> Error loading file for: <ccpnmr.Analysis.AnalysisProject ['AGR2']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml', >> mode 'r' at 0x59f23e8> >> Last xml tag read: ANAL.AnalysisSpectrum.dataSource >> Parser state was: reading >> Current object was: <ccpnmr.Analysis.AnalysisSpectrum ['AGR2', None]> >> >> >> If I try and open the backup project in your recommended way, renaming >> xyz_backup to xyz, the same set of messages appear as above, but with an >> added traceback message at the end >> >> Error during Exo link dereferencing. Object was: >> <ccp.molecule.MolSystem.Chain ['MS1', 'A']> >> values were: ['AGR2_pryank_2009-03-26-10-44-01-852_00001'] >> tag name was: molecule >> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS1']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml', >> mode 'r' at 0x58cbcf0> Last >> xml tag read: _StorageUnit >> Parser state was: postprocessing data >> Object stack was empty >> Error loading file for: <ccp.nmr.Nmr.NmrProject ['AGR2']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml', >> mode 'r' at 0x58c1f10> >> Last xml tag read: NMR.AtomSet.atoms >> Parser state was: reading >> Current object was: <ccp.nmr.Nmr.AtomSet ['AGR2', 1]> >> Error loading file for: <ccpnmr.Analysis.AnalysisProject ['AGR2']> >> Reading: <open file >> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml', >> mode 'r' at 0x4b4e828> >> Last xml tag read: ANAL.AnalysisSpectrum.dataSource >> Parser state was: reading >> Current object was: <ccpnmr.Analysis.AnalysisSpectrum ['AGR2', None]> >> Traceback (most recent call last): >> File >> "/home/pryank/programs/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisGui.py", >> line 224, in <module> >> main(projectDir, max_size, glDirect) >> File >> "/home/pryank/programs/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisGui.py", >> line 111, in main >> top.initProject(project) >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisPopup.py", >> line 1004, in initProject >> Analysis.initProject(self, project) >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py", >> line 257, in initProject >> self.initTopObjects(project) >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py", >> line 228, in initTopObjects >> self.analysisProject.isThreadingAllowed = False >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/api/Analysis.py", >> line 10239, in setIsThreadingAllowed >> >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5036, in load >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5070, in loadFrom >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 236, in loadTopObject >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 267, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py", >> line 4724, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccp/api/nmr/Nmr.py", >> line 16393, in getByKey >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5036, in load >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5070, in loadFrom >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 236, in loadTopObject >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 273, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py", >> line 4724, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccp/api/molecule/MolSystem.py", >> line 1278, in getByKey >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5036, in load >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py", >> line 5070, in loadFrom >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 236, in loadTopObject >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py", >> line 273, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py", >> line 4772, in loadFromStream >> File >> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py", >> line 5089, in delayedLoadLinksExo >> memops.general.Implementation.ApiError: Linked-to object with ID not found: >> <ccp.molecule.MolSystem.Chain ['MS1', >> 'A']>:molecule:AGR2_pryank_2009-03-26-10-44-01-852_00001 >> >> Best wishes, >> Pryank >> >> >> Wayne Boucher wrote: >> >>> Hello, >>> >>> I forgot to answer the question about the automated backup. Here is a >>> general blurb about backups. >>> >>> There are two types of backup. One backup happens when you do a save, so >>> it copies an existing *.xml file to *.xml.bak. To use those you just have >>> to rename the *.xml.bak as *.xml. Right now I'm not sure if all the >>> *.xml.bak taken together are guaranteed to be in a consistent state (i.e. >>> if you copy them all over then it will work). The main point of these >>> *.bak files is in case your disk is nearly full and writing out a new *.xml >>> file is not completed. So generally you probably wouldn't use these >>> backups. >>> >>> The other backup (and I think the one the question was about) is one you >>> can generate automatically (or on demand) via the Project --> Backup >>> dialog. The default here is that if your project is called Xyz then the >>> backup directory is Xyz_backup. When you open up a project you can just >>> use that directory rather than Xyz, i.e. instead of >>> >>> analysis Xyz >>> >>> you could do: >>> >>> analysis Xyz_backup >>> >>> This will warn you that some paths have changed. Instead of doing it this >>> way I'd generally recommend that instead you rename Xyz_backup to Xyz >>> (after backing up Xyz by hand just in case!). >>> >>> (You can also open up the backup via the Open Project dialog. You would >>> see the backup project row in the dialog coloured yellow instead of green, >>> but only because the project file is called Xyz.xml instead of >>> Xyz_backup.xml, which analysis can cope with perfectly well, but it's >>> warning you that this is not a standard naming.) >>> >>> Wayne >>> >>> On Wed, 15 Apr 2009, Dr. Pryank Patel wrote: >>> >>> >>> >>>> Hi all, >>>> >>>> >>>> >>> ... >>> >>> >>>> PS: is there any documentation on using the Backup system in Analysis? ie: >>>> how to load up a project from automated backup. >>>> >>>> >>>> >>>>