Dear contributors and users,
The well known visualizer JMOL allow to setup bond length in compound by tuning “Bond tolerance” and “Minimal bonding distance”, to visualize the bonds between atoms. This is very usefull feature, which I can’t find in Avogadro. Sometime I need to import the structure from “.xyz” ASCII file format and Avogadro fails to construct all bonds properly. I think this is due to fixed bond length for selected atoms. Is there any way to recalculate bonds with other tolerance or is it possible to construct manually bonds between atoms.
Many thanks in advance.
At the moment, Avogadro v1.x uses Open Babel to detect bonds and bond orders.
Avogadro v2 uses its own code, but there aren’t currently tolerances built into the algorithm.
Sounds like a good idea - can you post the suggestion on the tracker:
http://github.com/openchemistry/avogadrolibs/issues
Thank you for the kind and fast answer. Just to make clear, you want me to pull new feature requiest at github Avogadro project page, right?
https://github.com/cryos/avogadro/pulls
No, there’s no good way of doing this in the Avogadro 1 codebase.
In Avogadro v2, the bond perception is part of Avogadro. So I want you to submit to the new tracker:
http://github.com/openchemistry/avogadrolibs