Hello,
I've been helping a student to do an assignment in Analysis version 2.4 on NMRbox. NMRbox recently upgraded their system, which now includes V2.5 instead of V2.4. (Incidentally, we've found NMRbox very useful for collaborating, as multiple people can connect via VNC and view/control the virtual machine - it's the next best thing to standing around the same computer.)
Unfortunately, we now can't seem to open our projects in V2.5. When we try, we first get a warning that the location of refData has been changed. This is followed by a popup which reads
"Loading Project
Cannot add child - key already in use:
ccp.molecule.ChemComp.NonStdChemComp:<memops.Implementation.MemopsRoot
id:140380396808528>:('other', 'Acy')"
We also get some output in the terminal:
Error loading file for: <ccp.molecule.ChemComp.NonStdChemComp ['other', 'Acy']>
Reading: <open file '/usr/software/ccpnmr/ccpnmr2.5/data/ccp/molecule/ChemComp/other+Acy+ChemBuild_tjs23_2011-03-14-23-20-23-515_00001.xml', mode 'r' at 0x7face1315420>
Last xml tag read: CHEM.ChemComp.chemAtomSets
Parser state was: handling version compatibility
Object stack was empty
Error during Exo link dereferencing. Object was: <ccp.molecule.Molecule.MolResidue ['SasYr', 91]>
values were: ['msd_ccpnRef_2007-12-11-10-20-10_00001']
tag name was: chemComp
Error loading file for: <ccp.molecule.Molecule.Molecule ['SasYr']>
Reading: <open file '/home/nmrbox/rcooper/CCPN/SasYr7/ccp/molecule/Molecule/SasYr+SasYr1_rcooper_2020-04-01-09-14-25-180_00001.xml', mode 'r' at 0x7facef99b930>
Last xml tag read: _StorageUnit
Parser state was: postprocessing data
Object stack was empty
Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS2']>
Reading: <open file '/home/nmrbox/rcooper/CCPN/SasYr7/ccp/molecule/MolSystem/MS2+SasYr1_rcooper_2020-04-01-09-14-26-111_00001.xml', mode 'r' at 0x7facef99b9c0>
Last xml tag read: _StorageUnit
Parser state was: checking validity
Object stack was empty
Error loading file for: <ccp.nmr.Nmr.NmrProject ['SasYr1']>
Reading: <open file '/home/nmrbox/rcooper/CCPN/SasYr7/ccp/nmr/Nmr/SasYr1+SasYr1_rcooper_2020-04-01-07-06-06-934_00002.xml', mode 'r' at 0x7facef99b8a0>
Last xml tag read: NMR.AtomSet.atoms
Parser state was: reading
Current object was: <ccp.nmr.Nmr.AtomSet ['SasYr1', 1168]>
Any idea what might be going wrong? The error message seems to imply we have a non-standard residue at the C-terminus, but I'm pretty sure we haven't added anything like that. We'd be very grateful for any assistance! I am happy to send the project files if you need them.
Many thanks,
Alex Heyam
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