"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command?
If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command.
For example, the following command generate a ball and stick depiction of of the tyrosine molecule in SVG format:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-ball-stick.svg -xS 1 molecule converted
As a comparison, running the following command generates a normal skeleton depiction of of the same molecule in SVG format:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-skeleton.svg 1 molecule converted
Open both output files, tyrosine-skeleton.svg and tyrosine-ball-stick.svg, in a Web browser, you see the differences:
Note that "-xS" option was added in Open Babel 2.4 for SVG format.
⇒ "babel ... -o svg -xX" - Hide Implicit H in SVG
⇐ "babel ... -o svg -xi" - Show Atom Indices in SVG
⇑ "babel ... -o svg" - Generating SVG Pictures
2020-07-15, 650👍, 0💬
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Molecule Summary: ID: FYI-1000215 SMILES: C(CC[C@@H](C(=O)O)NC(=O) C1=CC=C(NCC2=CN=C3N=C(N) NC(=O)C3=N...