janosh
Interactive customization of bonds additions and deletions
Feature Request
Would like to be able to customize adding certain bonds or removing them, can't change this in the current situation
can you give more details? do you want to manually draw bonds between atoms? or do you want to show atoms only between certain pairs of elements but not others? something else?
Yes, that's exactly it. I would like to be able to manually draw bonds between atoms — specifically, to have the freedom to add or remove bonds between certain atoms.
i see. and should there be anything special about those custom bonds? should they have different thickness/color or custom labels? should the atoms they connect be highlighted in some way? what's your overall purpose?
Thank you for following up with such detailed questions. This is extremely helpful for clarifying my needs.
My Overall Purpose
My primary motivation is to accurately visualize complex crystal structures, specifically layered bimetallic oxides. The software's automatic bond detection is a great starting point, but it often produces chemically incorrect connections in these systems. This leads to misleading representations that need manual correction.
The errors fall into two main categories:
Incorrect Interlayer Bonds: Bonds are sometimes drawn between atoms in different layers that are too far apart. Incorrect Intralayer Bonds: More critically for my current case, incorrect bonds are often formed between metal atoms within the same layer. Therefore, the most crucial function I need is the ability to manually delete these incorrectly generated bonds to achieve a chemically accurate structure.
Regarding Special Features for Custom Bonds
To answer your specific questions, once the structure is corrected, the ability to add new, custom bonds to highlight specific interactions is also very valuable. Here’s how I envision the features for these custom bonds, in order of priority:
Bond Type (Most Important): The ability to define the bond as a single, double, or triple bond is essential. This allows for correct chemical representation. Alongside this, a dashed or dotted line style would be perfect for non-covalent interactions like hydrogen bonds.
Color and Thickness (Very Useful): Yes, allowing custom colors and thickness would be a fantastic feature for creating publication-quality figures, making it easy to distinguish or emphasize different types of interactions.
Custom Labels (Nice to Have): Adding a custom label (e.g., bond distance) directly onto the bond would be a powerful tool for detailed analysis and presentation.
Highlighting Atoms (Also a great idea): Highlighting the connected atoms is a great suggestion. This could be a simple toggle (on/off) when a custom bond is selected. It would help draw attention to specific sites.
In summary, my core need is a "Bond Edit Mode" where I can delete incorrect auto-generated bonds and add new, fully customizable bonds (type, style, color, etc.) to achieve an accurate and clear visualization.
Thank you so much for considering this comprehensive feedback!
I noticed that the current version already supports customizing whether chemical bonds form between atoms, which is very helpful.
Following up on this, I was wondering if it's possible to define different bond orders, such as double or triple bonds? If this isn't supported yet, are there any plans to add this functionality?