http://ligand-expo.rcsb.org/reports/F/FNK/FNK_ideal.pdb
has atoms O and O4 in close proximity; when I convert it using babel FNK_ideal.pdb FNK_ideal.mol2 using Open Babel 2.3.0 -- Oct 26 2010 -- 11:17:30 then the output mol2 file contains a bond between O and O4, the atom type for O becomes O.3 rather than O.2, and various of our later processing stages get very confused. FNK_ideal.pdb contains a full set of CONECT records; is there some way that I can get babel to use only those records and not add extra bonds based on atomic proximity? I see the -ac option to ignore CONECT records, but that's not what I want. Yours sincerely, Thomas Womack (Global Phasing) ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
