On Fri, 2005-04-08 at 17:19, Warren DeLano wrote: > However, are spaces legal within PDB field entries?
Looking at the PDB documentation, I see no explicit statement that they are *not* allowed. This page http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_76.html gives the 'standard' atom naming conventions, but these seem only to apply to atoms in amino acid residues, not to ligands or other het-groups. The example I gave was from heme; here, the standard naming for the four nitrogens at the centre of the pyridoxal ring seems to be " N A", " N B", " N C" , " N D". Gareth > They > would be expected cause problems because space is almost always used to > separate tokens. > > My suggestion would be to use a Python script to replace those spaces with > underscores... > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > > Gareth Stockwell > > Sent: Friday, April 08, 2005 6:25 AM > > To: pymol-users > > Subject: [PyMOL] PDB parse error? > > > > > > Warren, > > > > Using version 0.97, if I load a PDB with an atom like this: > > > > HETATM 2051 N A HEM B 400 -7.209 4.751 30.974 1.00 > > 16.78 N > > > > (e.g. in PDB 1f1c) > > > > Then Pymol loads the atom name as 'N' rather than 'N A'. Is > > there a way > > around this? > > > > Gareth > > > > -- > > Gareth Stockwell <gar...@ebi.ac.uk> > > European Bioinformatics Institute > > > > > > > > ------------------------------------------------------- > > SF email is sponsored by - The IT Product Guide > > Read honest & candid reviews on hundreds of IT Products from > > real users. > > Discover which products truly live up to the hype. Start reading now. > > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell <gar...@ebi.ac.uk> European Bioinformatics Institute
