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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