"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.
2020-07-15, 185👍, 0💬
What is chem.nlm.nih.gov ChemIDplus Database? chem.nlm.nih.gov ChemIDplus Database contains over 108...
Collections: Molecule FAQ SDF/Mol File FAQ Open Babel Tutorials PyMol Tutorials JSME Tutorials Inter...
How to build my own JSME editor Web Page? If you want to build your Web page and offer JSME as a mol...
What is chemdb.niaid.nih.gov's Molecule Compounds Against HIV? chemdb.niaid.nih.gov offers a searcha...