Hi,
> 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. > > You may try PDBsum. On the ligand page for 1h4p (NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA), you will find this file (link in picture sphere above jmol logo) : http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunRomLas.pl?pdb=1h4p_02_01&origin=pdbsum&script=YES&residues=-l&label_atoms=YES This file seems to contain the structure of the full ligand - but unfortunately in PDB format, with some CONECT at least. Otherwise, the cif file of 1h4p seems to contain all the needed information too. E.g. look for _pdbx_nonpoly_scheme.asym_id in http://www.rcsb.org/pdb/files/1H4P.cif : the asym_id G is only for the ligand NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA. Unfortunately, I'm not familiar enough yet with the mmcif format for additional hint, but I think you can get somehow the full ligand with the mmcif file. But anyway you will need many fixes to get the correct ligands structure for such tricky cases, as for the occupancy problem. You could try the CCL list too for this question. I hope it helps a bit :) Regards, Pascal
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