> Am I incorrectly running obfit, or am I misinterpreting what obfit does?
> Thanks for any help!
You're mis-interpreting what obfit does. It operates in 3D coordinates. So what
you're doing is okay - but if you then generate a PNG, you've thrown away the
3D coordinates.
If you want to see if obfit is operating correctly, open the resulting file in
PyMol or Avogadro or some similar 3D viewer.
If you want to highlight a SMARTS pattern in a depiction, you want something
different:
http://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure
<http://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure>
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://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-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
