"babel ... -o svg -xS" - Ball/Stick Depiction in SVG

Q

How to generate a ball and stick depiction of a molecule in SVG with the "babel" command?

✍: FYIcenter.com

A

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:

Tyrosine Molecule in skeleton and Ball/Stick Depictions

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

⇑⇑ Open Babel Tutorials

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