Dimitri Maziuk wrote > On 2015-11-19 05:28, Alexandre Fassio wrote: > >> Right, it's true. But, for example, if I have 8 ligands covalently bonded >> I >> would like to consider these 8 ligands as it were only one ligand and >> search >> on the mmCIF dictionary for a ligand that represents the 8 ligands >> together. >> Because by searching an ID for each ligand separately I wouldn't be >> considering the covalent bonds between them. > > I think our best option is to e-mail e.g.
> deposit@.rcsb > or > whatever other help address they have (deposit is the one for people > submitting structures -- but they will forward your question to the > right people) and ask "how do I find all entries containing e.g. > NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA" sequence. > > Dimitri > > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss Hi Dimitri, Alright, this is an option too. Meanwhile, I think that the best option is to evaluate each ligand separately. After checking on PDBSum as Pascal has suggested to me, I saw that the 8 ligands I had mentioned before are considered as a ligand called "NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA". Apparently, they don't have a ligand defined on the Chemical Component Dictionary that would represent these assembled ligands. Maybe, the only way to evaluate these ligands will be analysing one by one separately. Thank you a lot. Alexandre -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659057.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
