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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. >>> >>> >>>