I don't think it works this way, maybe somebody could confirm it. When you load a PDB, coordinates are parsed and ConnectTheDots() generates bonds. 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.
You may want to test that particular structure after removing all hydrogens. Also, if other prolines do not raise this issue, I would say that it's the structure that's problematic. 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. S On 01/20/2017 01:32 PM, Browning Nicholas John wrote: > The structure is a very poor one - but this shouldn't matter right? If the > bonding information is pulled from resdata then everything should be bonded > correctly without any inferred bonding distances. > > Nick > > Sent from my iPhone > >> On 20 Jan 2017, at 19:34, Stefano Forli <fo...@scripps.edu> wrote: >> >> Nick, >> if the PDB is the one you sent in your first email, it seems to have issues. >> >> When I open it in a viewer, I can see several spurious multiple bonds >> involving the >> hydrogens, which suggest that the structure is not optimal. >> >> I suspect the bond detection by distance gets messed up because of that. >> Have you found this issue with all prolines or just with this particular one? >> >> S >> >>> On 01/19/2017 02:46 PM, Geoffrey Hutchison wrote: >>> Can you send me the PDB file? >>> >>> Thanks, >>> -Geoff >>> >>> --- >>> Prof. Geoffrey Hutchison >>> Department of Chemistry >>> University of Pittsburgh >>> tel: (412) 648-0492 >>> email: geo...@pitt.edu >>> web: http://hutchison.chem.pitt.edu/ >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >> >> -- >> >> Stefano Forli, PhD >> >> Assistant Professor of ISCB >> Molecular Graphics Laboratory >> >> Dept. of Integrative Structural >> and Computational Biology, MB-112A >> The Scripps Research Institute >> 10550 North Torrey Pines Road >> La Jolla, CA 92037-1000, USA. >> >> tel: +1 (858)784-2055 >> fax: +1 (858)784-2860 >> email: fo...@scripps.edu >> http://www.scripps.edu/~forli/ >> >> ------------------------------------------------------------------------------ >> 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 > > -- Stefano Forli, PhD Assistant Professor of ISCB Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ 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
