Bond Atoms function distance not adjustable

[cook]

I believe this to be a bug with Avogadro:

Six carbon atoms 1.4 A apart are selected: when Build>Bond>Bond Selected Atoms function is chosen, each of the carbons is bound to the other five carbons. This issue persists for any Angstrom values set in Configure Bonding> Tolerance and Minimum Distance.

Environment Information

Avogadro version: 1.102.1
Operating system and version: OS 26.2 on Apple M4 pro chip

Expected Behavior

Bond function responds to changes in Configure Bonding settings.

Actual Behavior

Any distances in settings result in all selected atoms bonding to each other regardless of distance.

Steps to Reproduce

Input atomic coordinates and attempt Bond or Bond Selected function with varying distance settings.

Coordinates:
Fe 0.000000 0.000000 0.000000

C 1.400000 0.000000 1.600000

C 0.700000 1.212400 1.600000

C -0.700000 1.212400 1.600000

C -1.400000 0.000000 1.600000

C -0.700000 -1.212400 1.600000

C 0.700000 -1.212400 1.600000

C 1.400000 0.000000 -1.600000

C 0.700000 1.212400 -1.600000

C -0.700000 1.212400 -1.600000

C -1.400000 0.000000 -1.600000

C -0.700000 -1.212400 -1.600000

C 0.700000 -1.212400 -1.600000

[ghutchis]

If I remove all the bonds, then select all six of the atoms of those six-carbon rings and pick “Bond” it does what I’d expect .. bond the neighbors - with unsatisfied valence.

I’m heading to class, so I’d need to check what the “Bond Selected Atoms” command is supposed to do. I would certainly agree that what it’s currently doing is weird / wrong.

But both the “Bond Atoms” and “Remove Bonds” commands will only act on the selected atoms.

[ghutchis]

@ghutchis

I’m heading to class, so I’d need to check what the “Bond Selected Atoms” command is supposed to do.

It’s doing what it was supposed to do - create bonds between all selected atoms.

Is that useful? Guess I’ll need to look back through the change log and figure out when / why it was added:

Create Bond with distant atoms (too far to drag and drop)

I am trying to create a new bond to circularize a linear polymer. The only way I know to create a new bond is by dragging one atom and dropping it onto another, however these atoms are so far apart there is no way to have them visible on screen without adjusting the view, which I cant do while dragging the atom for bond creation. Is there a way to create a bond without the drag and drop method, or to adjust the view while dragging an atom? Thanks

Ah, the problem was creating an intentional bond between two separated atoms (e.g., to help with a ring polymer)

I can certainly understand why you find it confusing. We probably need some better wording.

[ghutchis]

@ghutchis

I can certainly understand why you find it confusing. We probably need some better wording.

Would “Connect Selected Atoms” with a tooltip be clearer? Or maybe something like “Force Bonds”?

I welcome some suggestions

[cook]

My main confusion came from the relationship between the Configure Bonding menu where you set distance tolerance and min distance and the Bond functions. What do the configure settings affect if not the Bond functions?

[ghutchis]

It absolutely affects the “Bond” command. The other command was a request from a user who wanted to select remote atoms and create a bond regardless of distance.

That’s why I was saying it’s a wording / documentation issue.