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
