> I don't think it works this way, maybe somebody could confirm it. Sorry that I didn't have a chance to respond yet. Bonding information is culled from OBResidueData, but ConnectTheDots is called later (e.g., in the frequent case that there are ligands or other non-residue atoms).
> Then there is a function to clean up extra bonds that shouldn't be there, but > I suspect that if you already filled all valences with these weird dual-bond > hydrogens, there is no > chance you're going to see the bonds you expect, no matter what the > resdata.txt file contains. Certainly if there are weird valences, then ConnectTheDots will start removing bonds based - longest first. > If you want to work with non optimal/distorted structures, you want to move > away from PDB and use something different that defines an explicit > connectivity table. This is, indeed, ideal advice. I can't see the "original PDB" file, only some small snippets. As I said, I'd prefer to debug the original file. Thanks, -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
