Hello,
Tim says that Analysis doesn't constantly scan for chemComps, so it may
take a re-load to notice. However, ChemBuild and then importing the XML
definitely works... Re PySide on Fedora, the Qt web pages, which we
mention on the web page, should help:
http://qt-project.org/wiki/PySide_Binaries_Linux
That error you got at the bottom is unfortunate. So the molecule name is
pretty long and there is a limit of 80 characters on the attribute that it
is complaining about. I don't know if it makes sense just to truncate the
name in this context to 80 characters (Wim could comment better about
that).
Wayne
On Tue, 24 Apr 2012, Lauriane Lecoq wrote:
> Hi all,
>
> I would like to assign a small molecule (an antibiotic) in ccpnmr, but I am
> wondering what is the best way to do it?
> I first checked if the molecule already exist in the "Small Compound" menu,
> but it is not the case.
>
> So, I tried to import the PDB file of the antibiotic (I created it with
> PRODRG and called it ERA) with Format Converter using " Import->single
> files->Chem compound -> PDB", and I got this error messages:
>
>
> Created era,other: neutral,none
> ERROR: no matches for names ['CB', 'C'].
> ERROR: no matches for names ['HAB', 'HAC', 'HAA'].
> ERROR: no matches for names ['HAE', 'HAD', 'HAF'].
> ERROR: no matches for names ['CAL', 'CAK'].
> ERROR: no matches for names ['CAY', 'CAJ'].
> etc...
> Created during import: 1 chemical component(s) (with 57 atoms, 60 bonds)
>
>
> Yet, I can not find the compound in ccpnmr in "Molecule -> Small Compounds".
> Should it normally appear in this menu or somewhere else?
>
>
> Then I tried another way:
> " Import->single files->Coordinates -> cns" (PDB format does not work)
>
> But I got this error message:
>
> Downloaded ChemComp other, Era from server
> http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&root=ccpn-chemcomp&pathrev=MAIN&path=/~checkout~/ccpn-chemcomp/data/pdbe/chemComp/archive/ChemComp/other/E,
> written to file
> /data/people/lecoq/nmr/ertapenem/ccpnmr_ertapenem2/ccp/molecule/ChemComp/other+Era+pdbe_ccpnRef_2011-10-12-02-56-11-827_00001.xml!
> Warning: selected IUPAC naming system for chemComp other,Era because XPLOR
> naming system does not exist.
> ERROR in ccpnmr.NameMapping.MoleculeMapping.__init__
> WARNING Error in clean-up of incorrectly created object.
> Data may be left in an illegal state
> 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/ccpnmr2.2/python/ccpnmr/format/gui/ImportExportFormatPopup.py",
> line 979, in ok
> if (not self.apply()):
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/gui/ImportExportFormatPopup.py",
> line 992, in apply
> returnValue = self.importExportFile(self.component) # If none, will do
> all components
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/gui/ImportExportFormatPopup.py",
> line 799, in importExportFile
> returnValue = rwFunc(*addArgs,**addKeywds)
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/DataFormat.py",
> line 1278, in readCoordinates
> self.getCoordinates()
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/DataFormat.py",
> line 4390, in getCoordinatesGeneric
> self.readSequence(**readSeqKeywds)
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/DataFormat.py",
> line 1071, in readSequence
> (createMoleculeDict,molSystemBonds) = self.checkMolecules()
> File
> "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/DataFormat.py",
> line 6662, in checkMolecules
> molMapping = NameMapping.MoleculeMapping(self.nameMapping, name =
> molName, formatName = newMolName)
> File "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/api/NameMapping.py", line
> 2901, in __init__
> func(self, value)
> File "/data/soft/ccpnmr/ccpnmr2.2/python/ccpnmr/api/NameMapping.py", line
> 3434, in setFormatName
> + ": %s" % (value,)
> ApiError: ccpnmr.NameMapping.MoleculeMapping.setFormatName:
> memops.Implementation.Line maximum length is 80 violated by value:
> (7Z,15E,17E)-N-[(2S,3S,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosa-7,15,17-trienamide
> Report failed <type 'exceptions.ImportError'>
>
>
> I was thinking about using the CcpNmr chembuild, but I did not manage to make
> it work, as one of the library is missing (Pyside) and I don't find it on
> Linux / fedora with the yum install command.
>
> Thank you for your help,
>
> Lauriane
>
> --
> Lauriane Lecoq
>
> phD student
> Laboratoire de Resonance Magnetique Nucleaire
> Institut de Biologie Structurale
> 41, rue Jules Horowitz
> 38027 Grenoble cedex 1
> Tel : (33)-4-38-78-96-33
> Email : [log in to unmask]
>
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