This isn't working because the Open Babel PDB code does not recognize space groups at the moment.
-Geoff On Jun 17, 2013, at 1:41 PM, Herbert Fruchtl <[email protected]> wrote: > Dear all, > > I want to find all the atomic positions in a pdb file, not just the symmetry > unique ones. I think the flag to do this is --fillUC, but it seems to have > problems with my PDB file, because I get the message: > > *** Open Babel Warning in Do > Cannot fill unit cell without spacegroup information ! > > My command is: > babel --fillUC strict csd_manthr01.pdb new.cif > > (I actually want a CASTEP cell file, but I know how to get this from cif). > The > PDB file comes from the Cambridge Structural Database, and the first few > lines are: > > HEADER CSD > COMPND MANTHR01 > AUTHOR Generated by a CDS Utility > CRYST1 8.909 14.625 8.060 90.00 96.53 90.00 P21/c 14 > ATOM 1 C MOL 8 3.618 5.399 1.991 1.00 0.00 > ... > > The space group information is presumably the P21/c in the CRYST1 line. Is > the > file wrong, can babel not handle it correctly, or do I need a different flag? > > Thanks in advance, > > Herbert > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
