Hi, I don't know if it can be useful for this specific problem, but the PDB has an advanced search interface which allows to use chemical information to query structures:
http://www.rcsb.org/pdb/search/advSearch.do?search=new Choose a Query Type -> Chemical component: ... You can use SMILES, InChi descriptors, or chemical component type, which include saccharide groups with various degrees of connections, and you can do substructure or similarity searches. For the records, each chemical compound that is deposited must have a unique ID, which will be in both the PDB and mmCIF files. Cheers, S On 11/20/2015 03:11 AM, Alexandre Fassio wrote: > Dimitri Maziuk wrote >> On 11/19/2015 05:07 PM, Alexandre Fassio wrote: >> >> ... Apparently, they don't have a >>> ligand defined on the Chemical Component Dictionary that would represent >>> these assembled ligands. >> >> As I understand it, they'll make a separate "compound" ligand for things >> that they see often, like in drugs -- I can't provide an example off the >> top of my head I'm afraid. For most "one-off" cases they will have them >> as separate ligands. But there should still be information in the >> struct_conn table in mmCIF for the macro structure. >> >> There's also chem_comp_atom.leaving_atom_flag in the ligand mmCIF, but >> that one's an even worse mess. :( >> >> -- >> Dimitri Maziuk >> Programmer/sysadmin >> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> OpenBabel-discuss mailing list > >> OpenBabel-discuss@.sourceforge > >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> >> signature.asc (197 bytes) >> <http://forums.openbabel.org/attachment/4659058/0/signature.asc> > > Hi Dimitri, > > I got it. Maybe the ligands was assembled to form only one and instead to > create a new id to this ligand they prefer to represent the used compounds > to represent it. I guess that they create IDs only when the compound is seen > often as you said. > > Thanks. > > > > > -- > View this message in context: > http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659061.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Stefano Forli, PhD Assistant Professor of Integrative Structural and Computational Biology, Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112F The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
