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Allow hydrogens to be shown above nitrogen in amine groups when it will otherwise obscure neighbouring covalent bonds #7054

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fusion809 opened this issue May 6, 2025 · 0 comments
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Micromolecules canvas Bucket: Micromolecules canvas related issues User`s Feedback

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fusion809 commented May 6, 2025

I love Ketcher, I use it to create skeletal formulas for Wikimedia Commons. It seems like the best open-source piece of software for drawing skeletal formulas available. One issue I have with it, however, is that it always shows hydrogens in amine groups horizontally next to the nitrogen, even when this obscures nearby lines (representing covalent bonds). I think Ketcher should, by default, show the H above the N in amine groups when showing it to the horizontal side of the N would obscure nearby lines.

Here is an example of what I mean. I am currently trying to create SVG graphics for methylphenidate's stereoisomers. Below is what I have at the moment. As you can see the H (for hydrogen) in the amine group is shown to the right of the N (for nitrogen). This causes some of the line that represents the nitrogen's covalent bond with the neighbouring carbon to be obscured.

Image

Currently, to get around this I need to bond amines with an additional carbon, export my graphic to SVG, and then in Inkscape I'll remove the added carbon bond and add the H above the N.

This is what I need to export from Ketcher:
Image

Then in Inkscape, I remove the N-methyl group and add a H on top of the N. This is the result of doing this:

Image

So, in summary, it would be great if hydrogens in amine groups were, by default, shown in a way that minimizes how much they obscure nearby covalent bonds. If you don't want to make this the default behaviour, it would be great if you could make it an optional behaviour, at least.

@AlexeyGirin AlexeyGirin added User`s Feedback Micromolecules canvas Bucket: Micromolecules canvas related issues labels May 7, 2025
@fusion809 fusion809 changed the title Allow hydrogens to be shown above nitrogen in amine groups when it will obscure neighbouring covalent bonds Allow hydrogens to be shown above nitrogen in amine groups when it will otherwise obscure neighbouring covalent bonds May 7, 2025
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