Pascal Muller-3 wrote > 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 > > ------------------------------------------------------------------------------ > > _______________________________________________ > OpenBabel-discuss mailing list
> OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss Hi Pascal, Thanks for the reply. I tried the PDBSum today to test what you mentioned. Unfortunately, the PDBSum seems to have only PDB files formats to download. Moreover, both the PDB and the CIF are not so suitable for me because I need to convert the file to MOL2 and I think that these formats could generate some errors after the conversion with Open Babel due to the lack of charge, valence, bond order information, etc (correct if I'm wrong). Anyway, the PDBSum gave some insights and I liked the way that they treat the covalently bonded ligands. Thanks for the help. -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659056.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
