Hello,
The problem is that the standard Analysis release has Acy included in it, and the Metabolomics test project also has Acy included in it, and the program does not like having duplicates. I guess the easiest option here (to at least get going) is to delete, or better, rename, the Metabolomics test project version (hopefully that way around makes more sense, anyway). Thus in the directory
CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/molecule/ChemComp
Do something like:
mv other+Acy+msd_ccpnRef_2007-12-11-10-14-27_00018.xml other+Acy+msd_ccpnRef_2007-12-11-10-14-27_00018.xml.orig
There might be the odd other file like that as well.
Wayne
On 26 Feb 2014, at 13:43, Eva Caamano wrote:
> Dear all,
> Apologies if this problem has come up before. I am new to both NMR and CCPNmr. I am trying to use the metabolomics package but when I tried to open the project as it is said in the tutorial, I get the following error:
> "Cannot add child-Key already in use: ccp.molecule.ChemComp.NonSTDChemComp:<memops.Implementation.MemopsRoot id:4466173904>:('other','Acy')
>
> I have seen that a similar problem was solved in the past by using the python script: "deleteRedundantConstraintItems" but I could not fix it. I get this information from running it:
>
> " Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Applications/ccpnmr/CCPN_Metabolomic_v1.3/deleteRedundantConstraintItems.py", line 4, in deleteRedundantConstraintItems
> AttributeError: 'str' object has no attribute 'nmrConstraintStores'
> Error loading file for: <ccp.molecule.ChemComp.NonStdChemComp ['other', 'Acy']>
> Reading: <open file '/Applications/ccpnmr/ccpnmr2.3/data/ccp/molecule/ChemComp/other+Acy+ChemBuild_tjs23_2011-03-14-23-20-23-515_00001.xml', mode 'r' at 0x1097560c0>
> 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 ['arginine', 1]>
> values were: ['msd_ccpnRef_2007-12-11-10-20-10_00007']
> tag name was: chemComp
> Error loading file for: <ccp.molecule.Molecule.Molecule ['arginine']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/molecule/Molecule/arginine+metabo2_fchignola_2009-07-24-11-50-53-251_00001.xml', mode 'r' at 0x109756030>
> Last xml tag read: _StorageUnit
> Parser state was: postprocessing data
> Object stack was empty
> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['arginine']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/molecule/MolSystem/arginine+metabo2_fchignola_2009-07-24-11-50-27-221_00001.xml', mode 'r' at 0x1096b6f60>
> Last xml tag read: _StorageUnit
> Parser state was: checking validity
> Object stack was empty
> Error loading file for: <ccp.nmr.Nmr.NmrProject ['metabo2']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/nmr/Nmr/metabo2+metabo2_fchignola_2009-07-24-11-49-23-331_00002.xml', mode 'r' at 0x108429ed0>
> Last xml tag read: NMR.AtomSet.atoms
> Parser state was: reading
> Current object was: <ccp.nmr.Nmr.AtomSet ['metabo2', 1]>
> Error loading file for: <ccp.molecule.ChemComp.NonStdChemComp ['other', 'Acy']>
> Reading: <open file '/Applications/ccpnmr/ccpnmr2.3/data/ccp/molecule/ChemComp/other+Acy+ChemBuild_tjs23_2011-03-14-23-20-23-515_00001.xml', mode 'r' at 0x1097560c0>"
> 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 ['arginine', 1]>
> values were: ['msd_ccpnRef_2007-12-11-10-20-10_00007']
> tag name was: chemComp
> Error loading file for: <ccp.molecule.Molecule.Molecule ['arginine']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/molecule/Molecule/arginine+metabo2_fchignola_2009-07-24-11-50-53-251_00001.xml', mode 'r' at 0x109756030>
> Last xml tag read: _StorageUnit
> Parser state was: postprocessing data
> Object stack was empty
> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['arginine']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/molecule/MolSystem/arginine+metabo2_fchignola_2009-07-24-11-50-27-221_00001.xml', mode 'r' at 0x1096b6f60>
> Last xml tag read: _StorageUnit
> Parser state was: checking validity
> Object stack was empty
> Error loading file for: <ccp.nmr.Nmr.NmrProject ['metabo2']>
> Reading: <open file '/Applications/ccpnmr/CCPN_Metabolomic_v1.3/CCPN_Metabolomic_v1_3/ccp/nmr/Nmr/metabo2+metabo2_fchignola_2009-07-24-11-49-23-331_00002.xml', mode 'r' at 0x108429ed0>
> Last xml tag read: NMR.AtomSet.atoms
> Parser state was: reading
> Current object was: <ccp.nmr.Nmr.AtomSet ['metabo2', 1]>
>
> I will be very grateful if you could help me to solve this problem.
> Many thanks for your time,
> Eva Caamano
