Structure Display Command on Open Babel GUI

Q

How to change the display command on Open Babel GUI?

✍: FYIcenter.com

A

By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error:

Obgui Error: 
Execution of command "firefox ..." failed. 
System cannot find the file.

To fix the problem, you can change the display command as shown in this tutorial.

1. Start Open Babel GUI and go to "View > Configure Structure Display" menu. You see a small window showing the current display command.

2. Enter a new command to use a different browser. For example, enter the following to use the Google Chrome browser:

\Progra~1\Google\Chrome\Application\Chrome file:///
C:\Users\fyicenter\AppData\Local\Temp/gui.svg

3. Enter a new molecule in the input section on the left.

4. Click to select the "Display in ..." checkbox in the output section on the right.

5. Click the "CONVERT" button. You see the molecule structure displayed in the Google Chrome browser.

Open Babel GUI - Change Structure Display

⇒ Understanding "babel" Command Line Syntax

⇐ Run Open Babel GUI on Windows

⇑ Running Open Babel on Windows

⇑⇑ Open Babel Tutorials

2022-05-31, 595👍, 0💬

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Where to find FAQ (Frequently Asked Questions) on doing Stereochemistry with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on doing Stereochemistry with Open Babel. What Is Stereochemistry Read Stereoinformation from Input Stereo Per... 2022-05-31, 691👍, 0💬

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Structure Display Command on Open Babel GUI
How to change the display command on Open Babel GUI? By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error: Obgui Error: Execution of command "firefox ..." failed. System cannot find the file. To fix the problem, you can cha... 2022-05-31, 596👍, 0💬

What Is Stereochemistry
What Is Stereochemistry? Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements. Here are some stereoisomers listed in the picture below: Example of Stereoisomers You can do stereochemistry with Open Babel... 2022-11-09, 570👍, 0💬

Hash Bond with Solid Line
Why Hash Bond with a Solid Line used by Open Babel? Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond. Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure. Hash-with-Solid-Line FYICenter.com ... 2022-07-26, 540👍, 0💬

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How stereoinformation is being read from input data by Open Babel? Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level. 2D: Stereoinformation in 2 dimension is defined by bond style as wedg... 2022-11-16, 530👍, 0💬

Stereo Perception Performed by Open Babel
What is stereo perception performed by Open Babel? Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data. Stereo perception is performed in the following order of precedence: 1. Constructing stereo centers with 3D ster... 2022-11-16, 528👍, 0💬

Molecule FYI-1000237
Molecule Summary: ID: FYI-1000237 SMILES: CCCCC Received at FYIcenter.com on: 2021-02-04 2021-02-17, 375👍, 0💬

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