Was this the first time you opened it up (in v2)?
That message is implying that there is more than one DNA U XML file in
your project. Now one such XML file is in the reference data (in the
directory /Applications/ccpnmr/ccpnmr2.0/data/ccp/molecule/ChemComp). The
second one might be in your own project directory (in the directory
/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/molecule/ChemComp I would
guess). Either that or somehow there are two DNA U XML files in the
reference data directory. I'm not sure how that would happen. But I'm
not sure how you might have ended up with a DNA U XML file in your project
directory, unless somehow it was part of the conversion from the v1 to v2
that did this.
If you look for files that match DNA+U+*.xml then you will hopefully find
the two. If so then you can delete the second one (hopefully the one in
your project directory) and everything should be ok. Well, rather than
delete just move somewhere else, in case I am analysing this incorrectly.
Wayne
On Wed, 7 Jan 2009, Johnny Croy wrote:
> Hi Wayne,
>
> Got a funny error opening one of my converted projects. Got a pop up
> windows that reads,
>
> Cannot add child - key already in use:
> ccp.molecule.ChemComp.StdChemComp"<memops.Implementation.MemopsRoodId:
> 79065008>:('DNA'.'U')
>
> This also came up in the terminal window.
>
> >>> Error loading file for: <ccp.molecule.ChemComp.StdChemComp
> ['DNA', 'U']>
> Reading: <open file '/Applications/ccpnmr/ccpnmr2.0/data/ccp/molecule/
> ChemComp/DNA+U+msd_ccpnRef_2007-12-11-10-13-17_00008.xml', mode 'r' at
> 0x49c13c8>
> 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 ['6mer', 6]>
> values were: ['msd_ccpnRef_2007-12-11-10-13-16_00002']
> tag name was: chemComp
> Error loading file for: <ccp.molecule.Molecule.Molecule ['6mer']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> molecule/Molecule/6mer
> +SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00012.xml', mode
> 'r' at 0x49bff98>
> Last xml tag read: _StorageUnit
> Parser state was: postprocessing data
> Object stack was empty
> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS1']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> molecule/MolSystem/
> MS1+SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00114.xml',
> mode 'r' at 0x49bff08>
> Last xml tag read: _StorageUnit
> Parser state was: checking validity
> Object stack was empty
> Error loading file for: <ccp.nmr.Nmr.NmrProject
> ['SpPot1pN_Bound_DNA_assign']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> nmr/Nmr/SpPot1pN_Bound_DNA_assign
> +SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00117.xml', mode
> 'r' at 0x3a309f8>
> Last xml tag read: NMR.AtomSet.atoms
> Parser state was: reading
> Current object was: <ccp.nmr.Nmr.AtomSet
> ['SpPot1pN_Bound_DNA_assign', 1]>
> Error loading file for: <ccp.molecule.ChemComp.StdChemComp ['DNA',
> 'U']>
> Reading: <open file '/Applications/ccpnmr/ccpnmr2.0/data/ccp/molecule/
> ChemComp/DNA+U+msd_ccpnRef_2007-12-11-10-13-17_00008.xml', mode 'r' at
> 0x49c1920>
> 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 ['6mer', 6]>
> values were: ['msd_ccpnRef_2007-12-11-10-13-16_00002']
> tag name was: chemComp
> Error loading file for: <ccp.molecule.Molecule.Molecule ['6mer']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> molecule/Molecule/6mer
> +SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00012.xml', mode
> 'r' at 0x49c1188>
> Last xml tag read: _StorageUnit
> Parser state was: postprocessing data
> Object stack was empty
> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS1']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> molecule/MolSystem/
> MS1+SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00114.xml',
> mode 'r' at 0x49c10f8>
> Last xml tag read: _StorageUnit
> Parser state was: checking validity
> Object stack was empty
> Error loading file for: <ccp.nmr.Nmr.NmrProject
> ['SpPot1pN_Bound_DNA_assign']>
> Reading: <open file '/Users/jec/CCPNMR2/SpPot1pN_Bound_DNA_assign/ccp/
> nmr/Nmr/SpPot1pN_Bound_DNA_assign
> +SpPot1pN_Bound_DNA_assign_user_2008-09-05-17-51-31_00117.xml', mode
> 'r' at 0x3d0ed10>
> Last xml tag read: NMR.AtomSet.atoms
> Parser state was: reading
> Current object was: <ccp.nmr.Nmr.AtomSet
> ['SpPot1pN_Bound_DNA_assign', 1]>
>
> Any ideas? My guess is a botched conversion job.
>
> Johnny
>
> ------------------------------------------------------------
> Johnny Eugene Croy, Ph.D.
> Research Associate
> Wuttke Lab
>
> University of Colorado, Boulder
> Department of Chemistry and Biochemistry
> UCB 215
> Boulder, CO 80309-0215
>
> Lab: (303) 492-2369
> Mobile: (303) 304-6069
> ------------------------------------------------------------
>
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