Aligning molecules and dummy atoms

[ghutchis]

@thowe99

What could make it alot easier is the ability to select an atom and reset it to have xyz coordinates 0,0,0. and a second atom and align directly to a specific axis.

This is exactly the align tool: Align Tool - Avogadro

@thowe99

An additonal tool that I would love is the ability to add atoms to specific positions relative to other atoms. To be able to select two atoms and place a third such that its at a certain angle and distance using one of the atoms as a vertex. Or select three atoms to define a plane and add a fourth using a plane and a vertex from the selected three atoms.

Interesting idea. This sounds more like a menu command than a tool, but I definitely see the use case. At one point, we had an idea for a “z-matrix tool” that worked a bit like this.

@thowe99

Final idea. To be able to click on the red-gren-blue axis arrows in the bottom left to align an axes vertically and horizontally so it is possible to make clean 90 degree rotations

I’m not sure I quite understand. You want to click the arrows to align the camera view… how does that connect with making rotations? If you want to make specific angle rotations, you can do that in the manipulate tool: