Ahhh, that makes sense. Thank you for the clarification!
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________________________________
From: Geoffrey Hutchison <[email protected]>
Sent: Wednesday, June 6, 2018 5:55:40 PM
To: John Michael Bruning
Cc: [email protected]
Subject: Re: [Open Babel] obfit question
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
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [email protected]<mailto:[email protected]>
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/
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