OK, the Chemical compounds route is likely the best way to proceed.  And after I have just tried it myself with your PDB it reminded me that the best format for importing this is mol2 (yes, not mol, or PDB, I can't remember why).  I converted the PDB file to mol2 using OpenBabel and it then imported ok with the Format Converter (I took all the defaults and answered no to the question about adding a chemCompVar).  This created a small compound, not a molecule, so you then have to go into the Analysis Molecule --> Molecules dialog (this takes some seconds to open) in the Small Compounds tab and find the compound in that long list (the default name on import in FC is UNK0 but you might have given it a better name).  If you then click on the Add Compound button it will then create a molecule.  If you then go into the Chains tab you can also create a Chain using this Molecule.

Wayne

On 27 Feb 2014, at 15:05, Almeida, Teresa wrote:

> Thank you for your kind reply.
> 
> My first attempt was made by trying: 
> Import-> Format Converter -> Import -> Single files -> Chemical compounds -> pdb, 
> 
> and I got the error that I emailed before. However, it works if I do the same but importing .mol instead of .pdb, the only problem is I don't get the connections/bonds between the atoms.
> 
> Below are the errors I got after your suggestions:
> 
> Import-> Format Converter -> Import -> Single files ->coordinates -> pdb
> 
> Error: /home/talmeida/ZINC08389070.pdb is not a file originating from PDB. Cannot be read.
> Exception in Tkinter callback
> Traceback (most recent call last):
>  File "/usr/local/prog/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
>    return self.func(*args)
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 981, in ok
>    if (not self.apply()):
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 994, in apply
>    returnValue = self.importExportFile(self.component) # If none, will do all components
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 801, in importExportFile
>    returnValue = rwFunc(*addArgs,**addKeywds)
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/DataFormat.py", line 1313, in readCoordinates
>    self.selectMolSystem()
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/general/TopShared.py", line 137, in selectMolSystem
>    urlFile = 'SelectMolSystem')
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/general/MultiDialog.py", line 131, in SelectionList
>    return self.SelectionListFunction(guiParent,*args,**kw)
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/MultiDialog.py", line 142, in SelectionListFunction
>    popup = SelectionListPopup(guiParent,*args,**kw)
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/SelectionListPopup.py", line 97, in __init__
>    TemporaryBasePopup.__init__(self,parent = parent, title = title, modal = modal, transient=True)
>  File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/memops/gui/BasePopup.py", line 86, in __init__
>    Tkinter.Toplevel.__init__(self, parent, *args, **kw)
>  File "/usr/local/prog/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1975, in __init__
>    BaseWidget.__init__(self, master, 'toplevel', cnf, {}, extra)
>  File "/usr/local/prog/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1932, in __init__
>    (widgetName, self._w) + extra + self._options(cnf))
> TclError: bad window path name ".119398056.130174272"
> 
> Import-> Format Converter -> Import -> Single files -> coordinates -> Pseudo pdb
> 
> ##############################################
> # FormatConverter: executing readCoordinates #
> ##############################################
> 
> 
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error converting '     ' to integer: set to 0.
> Error: no complete chain linking found between coordinates and chains. Aborting coordinate reading.
> 
> Kind regards
> Teresa Almeida
> 
> PhD student
> Department of Chemistry/Institute of Integrative Biology
> University of Liverpool
> Liverpool
> L69 7ZD
> United Kingdom
> 
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Wayne Boucher [[log in to unmask]]
> Sent: 27 February 2014 10:27
> To: [log in to unmask]
> Subject: Re: import small molecules
> 
> Hello,
> 
> That’s probably the Format Converter being strict about what the PDB format is.  Did you try “Pdb” or “PseudoPdb”?  The latter is more lenient.
> 
> Alternatively, you can try importing it in the Analysis Structure —> Structures dialog in the Ensembles tab.  There is an Import button at the bottom.  I think this will create the molecule, anyway, if it doesn’t already exist.
> 
> Wayne
> 
> On 27 Feb 2014, at 10:06, Teresa Almeida <[log in to unmask]> wrote:
> 
>> I was trying to import a small molecule into CCPNMR from a pdb file but I get the following error:
>> 
>> ############################################
>> # FormatConverter: executing readChemComps #
>> ############################################
>> 
>> 
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Error converting '    ' to integer: set to 0.
>> Created test1,other: neutral,none
>> Exception in Tkinter callback
>> Traceback (most recent call last):
>> File "/usr/local/prog/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
>>   return self.func(*args)
>> File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 981, in ok
>>   if (not self.apply()):
>> File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 994, in apply
>>   returnValue = self.importExportFile(self.component) # If none, will do all components
>> File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 801, in importExportFile
>>   returnValue = rwFunc(*addArgs,**addKeywds)
>> File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/DataFormat.py", line 1559, in readChemComps
>>   self.makeChemComp()
>> File "/usr/local/prog/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/DataFormat.py", line 14476, in makeChemComp
>>   for chemCompVar in chemAtom.chemCompVars:
>> AttributeError: 'NoneType' object has no attribute 'chemCompVars'
>> start generating output :  ccp.molecule.ChemCompCoord.ChemCompCoord
>> start generating output :  ccp.molecule.MolSystem.MolSystem
>> start generating output :  ccp.general.DataLocation.DataLocationStore
>> start generating output :  ccp.nmr.Nmr.NmrProject
>> start generating output :  ccp.molecule.ChemComp.NonStdChemComp
>> start generating output :  ccp.molecule.Molecule.Molecule
>> start generating output :  ccp.molecule.MolSystem.MolSystem
>> start generating output :  ccpnmr.Analysis.AnalysisProject
>> 
>> Could you give me any clues about what is going on? My CCPNMR version is 2.3.1 and I cannot use ChemBuild since I am using CentOS and it is not compatible. Also it would be nice if you could make a webserver that could convert pdb to xml for the users that cannot use ChemBuild.
>> 
>> Many thanks
>> Teresa