Hello,
The immediate problem (there might be others!) is that the mailing address has an accent (acute e, I think) in it. Python is notoriously bad at unicode. I don’t know how the PDBe generally deal with accents, but in this case it might be best to leave it out.
Wayne
On 6 Jan 2015, at 17:04, Brian Smith <[log in to unmask]> wrote:
> Beate,
>
> I've successfully submitted a couple of projects through AutoDep at PDBe recently. I did have a "failure to unpack" type of message with one, but this was solved when I made a clean archive of the project from within analysis. I think that if you just tar & gzip your project externally, AutoDep may be confused by additional unlinked .xml files and/or the .bak files it contains.
>
> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
> Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
> College of Medical, Veterinary & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089
> ----------------------------------------------------------------------
> The University of Glasgow, charity number SC004401
>
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Beate Bersch [[log in to unmask]]
> Sent: 06 January 2015 15:57
> To: [log in to unmask]
> Subject: problems with data submission
>
> Dear all
> I encounter some problems when trying to submit my data:
> AutoDep does not accept my zipped ccpnmr project
> When I try to export an NMR Star file, this does not work neither:
>
> Using CCPN version 2.1.2, NMR-STAR version 3.1.
> Warning: No Ccpn__2_1_2__To_NmrStar__3_1__ conversion class available, using Ccpn_To_NmrStar default.
> Warning: No Ccpn__2_1_2__To_NmrStar__3_1__ constants dictionary available, using Ccpn_To_NmrStar default.
> Using CCPN version 2.1.2, NMR-STAR version 3.1.
> Warning: No Ccpn__2_1_2__To_NmrStar__3_1__ conversion class available, using Ccpn_To_NmrStar default.
> Warning: No Ccpn__2_1_2__To_NmrStar__3_1__ constants dictionary available, using Ccpn_To_NmrStar default.
> Warning: no PDB_REMED atomSysName available for 'A.35.CG*', trying IUPAC.
> Warning: no PDB_REMED atomSysName available for 'A.53.CD*', trying IUPAC.
> Warning: no PDB_REMED atomSysName available for 'A.35.CG*', trying IUPAC.
> Warning: no PDB_REMED atomSysName available for 'A.53.CD*', trying IUPAC.
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/data/soft/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
> return self.func(*args)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/ccpnmr/eci/EntryCompletionFrame.py", line 9151, in exportNmrStar31
> nmrStarExport.createFile(fileName)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 201, in createFile
> self.loopSaveFrameData(0)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 292, in loopSaveFrameData
> self.setSaveFrameData(self.nmrStarSfDict['name'])
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 407, in setSaveFrameData
> self.loopStarLevelObjects('saveFrame',saveFrameName,ccpnLoopInfo,self.writeStarSfDict,self.nmrStarSfDict)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 697, in loopStarLevelObjects
> if not self.setTableData(tableName,saveFrame = starElement):
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 442, in setTableData
> self.loopStarLevelObjects('table',tableName,ccpnLoopInfo,self.writeStarTableDict,self.nmrStarTableDict,starElement = table)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 661, in loopStarLevelObjects
> self.setStarTags(starElement,starElementName,tagNames,writeTags,conditionalTags,presetValues,ccpnLoopInfo,parentCcpnLoopInfo,writeStarElementDict,nmrStarElementDict)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1142, in setStarTags
> value = returnFunc(value)
> File "/data/soft/ccpnmr/ccpnmr2.4/python/pdbe/nmrStar/IO/nmrStarDict.py", line 320, in <lambda>
> 'Address_1': [None,lambda x = value: returnStarLine(x,length = 127),None,True], # The mailing address of the author of the entry to whom correspondence should be addressed$ line 1 of 3.
> File "/data/soft/ccpnmr/ccpnmr2.4/python/ccp/format/nmrStar/util.py", line 145, in returnStarLine
> value = str(value)
> UnicodeEncodeError: 'ascii' codec can't encode character u'\xe9' in position 9: ordinal not in range(128)
>
>
> I have no idea whether A.35.CG* (35 is a valine but both CG1 and CG2 are both assigned) and 53.CD* (leucine, both CD1 and CD2 are assigned) are the reason for the error and, if so, where this information is hidden. It is really frustrating to encounter these difficulties once everything is finished and a lot of time is spent in order to fill in all the details of the Entry.
> Thanks a lot
>
> Beate
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