"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

2020-07-15, 1403🔥, 0💬

Enantiomers Isomer Example
What are examples of Enantiomers Isomers? The picture below gives an example of Enantiomers Isomers: Stereoisomers > Enantiomers (Mirror Images) The molecule on the left is (R)-Lactic Acid with a chiral C in (R)-configuration, or right-hand configuration, or clockwise configuration. The molec... 2020-08-03, 3732🔥, 1💬

What Is Radical Molecule
What is Radical Molecule? A Radical molecule, also called free radical, is molecule that has one or more radical centers. A Radical center is an atom in a molecule that has an unpaired valence electron, or odd number of valence electrons (including both bounded and unbound electrons). When writing t... 2020-08-03, 3087🔥, 1💬

Rotamers Example
What are examples of Rotamers? The picture below gives an example of Rotamers: Stereoisomers > Diastereomers > Conformational > Rotamers ⇒ Molecule Presentation and Identification ⇐ Enantiomers Isomer Example ⇑ Introduction to Molecules ⇑⇑ Molecule FAQ 2020-07-07, 2530🔥, 0💬

Constitutional Isomer Example
What are examples of Constitutional Isomers? The picture below gives an example of Constitutional Isomers: Constitutional or Structure Isomers The molecule on the left is N-Butane, also known as Normal Butane, which is a flammable, colorless, mostly nontoxic gas with a natural gas odor. The molecule... 2020-08-03, 2366🔥, 1💬

"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command? If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command. Here is ... 2020-07-22, 1892🔥, 0💬

"babel ... -o svg -xP300" Bug - width="px" height="px"
Why "babel ... -o svg -xP300" command is not able scale a molecule SVG image? The "babel ... -o svg -xP300" command has a code bug that results incorrect attributes, width="px" height="px", in the top level "svg" element. in both Open 2.3 and 2.4 releases. However, "obabel ... -o svg -xP300" command... 2020-07-22, 1868🔥, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given square area? The default behavior of Open Babel 2.4 is different than 2.3 regarding scaling and centering SVG images. With Open Babel 2.4, the molecule SVG image is defaulted in the center of 200x200 square. With Open Babel 2.3, the molecule SV... 2020-07-22, 1610🔥, 0💬

"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 ... 2020-07-15, 1404🔥, 0💬

"babel ... -o svg -xC" - Hide Terminal C in SVG
How to hide those C symbols for terminal carbon atoms in SVG with the "babel" command? If you want to hide those C symbols for terminal carbon atoms in SVG format, you can use the "-o svg -xC" option with the "babel" command. Here is how the "-xC" option is described in Open Babel help document: "C ... 2020-07-22, 1377🔥, 0💬

All rights in the contents of this web site are reserved by the individual author. fyicenter.com does not guarantee the truthfulness, accuracy, or reliability of any contents.