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Bonds not detected and displayed

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.2.0
Operating system and version: Windows 10 64 bit

Expected Behavior

Bonds not detected and displayed from an .xyz file.
I have found this is an increasing problem. The latest example I have an aromatic ring with four of the C-C bonds complete, but the final two are not displayed, despite being the same length as all the rest. The disconnected atom is also disconnected from the H atom it is meant to be bonded to. There are other bonds missing that would also be expected, but aromatic ring is the most important one.

Actual Behavior

Bonds not displayed.

Steps to Reproduce

I am not certain what I need to do, but the file I am using appears to consistently have this problem.

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin) - how to upload files here?

You can upload files to other services and paste the link here. Without the file, it’s impossible to debug.

Try this one: https://www.dropbox.com/s/9sn0fdesmjy4wjc/Mo01R.xyz?dl=0 I hope it works for you and I hope it replicates the effect:

The distances between those particular carbon atoms are ~1.1Å so the bond perception algorithm is very much unhappy. I have no doubt that it tried to assign triple bonds around the ring, plus the hydrogen and couldn’t make it all add up. (A typical CC triple bond would be ~1.2Å.)

The bond perception algorithm isn’t perfect, but if the tolerance is made too loose, a lot of bad PDB / crystal structure files end up with bad bonding too.

Can I ask what program / method produced this file?