How to draw stick structure on Ubuntu 22?


I have installed Avogadro2 1.95.1 on Ubuntu 22.04 with sudo apt-get install avogadro.

I would like to draw either a standard chemical structure or a stick version of it.
However, the version I have does not show the stick option only as in the online manual: I have wireframe, stick and balls, and licorice. These are not the same as stick. In particular, no double bonds are displayed.

Is there a plugin to add or a better version of the one I have?

Thank you

I’m not sure quite what you want. Licorice is what most people mean when they say “sticks.”

And yes, the default is to show multiple bonds.

Can you upload an example image of what you want to see?

Essentially, I need to draw saccharin (left of figure). But the liquirice version is that on the center. To note that (1) the gradient of the colour might confuse the audience at hand and (2) there are no double bonds.
The stick look from the website looks better (left).

Maybe I need to tweak some options?

Thank you

If you’re trying to make 2D chemical drawings, Avogadro is not your app. We do 3D structures. I’d suggest ChemDoodle or ChemDraw JS, for example.

You’re correct that the licorice / stick version in Avogadro 2 doesn’t have an option to display multiple bonds. That’s mostly because in other programs, that depiction rarely indicates multiple bonds (vs. the default ball-and-stick depiction).

So are you looking for the strictly 2D line drawing? Or do you want a 3D version with licorice but with multiple bonds? Thanks.

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I see. I was planning to spice up the drawing by using the 3D features of licorice/stick but showing the multiple bands. If it is not possible, then I’ll have to stick with the 2D editors. Thanks

It wouldn’t be hard if you’re willing to install the AppImage. But I’d love to see an example of what you want. In general, when I’ve had multiple bonds with sticks / licorice instead of balls-and-sticks, it looks a bit weird.

I agree. I think I’ll stick with the 2D version and use Avogadro for real 3D imaging (space-filled etc)… Thank you

And as I said … if you see an image that you like the style, please post it as a suggestion. Thanks!