Dimitri Maziuk wrote > On 2015-11-18 05:05, Alexandre Fassio wrote: > >> For example, a cellobiose can be represented as two glucoses (GLCs). >> Thus, >> it is difficult to know without a previous knowledge, which ligand is >> represented by these two GLCs. >> >> In another case, I had a PDB with 8 ligands covalently bonded and I don't >> know which ligand in the CIF dictionary represents these 8 ligands. > > Well, if you download an mmCIF for the ligand, > _chem_comp.pdbx_subcomponent_list field should contain the 3-letter > codes. I don't know if they've gone through their entire ligand library > and filled in that field in every "compound component", though. > > E.g. in some cases, like ALA_NH2, they list NH2 as a separate chem. > comp. instead. > > Dimitri > > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list
> OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 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. -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659052.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
