For a small group of small organic molecules, I would like to use Avogadro to display short intermolecular contacts directing their packing patterns; separately from normal Hydrogen bonding pattern. For example, to indicate intermolecular C(aryl)-H interactions.

It is known to me that this may be achieved with the freely accessible software Mercury by the CCSD (described here), too. Yet, both for the sake of consistency with other drawings already prepared, as well some curiosity if Avogadro equally may provide this, I whish to address the question here. The sole contribution in the software's mailing list partially relevant to this topic (here), dating back 2013, exludes even the indication of non-classical H-bonds.

To solve this problem, both the "classical version" (currently 1.2.0), as well as the more recent version Avogadro² (1.90.0) were accessed.

  • $\begingroup$ So, what's the question? How to represent an interaction between any two atoms of your choice? $\endgroup$
    – Anon
    Commented Apr 11, 2017 at 17:58
  • $\begingroup$ It's a good feature suggestion, but it's not implemented in either version at the moment. I'd suggest, for example, suggesting the feature here for Avogadro v1.x or here for Avo2. $\endgroup$ Commented Apr 11, 2017 at 18:16
  • $\begingroup$ And as you seem to know, there's a mailing list and a discussion board specifically for Avogadro questions. $\endgroup$ Commented Apr 11, 2017 at 18:17
  • 5
    $\begingroup$ I'm voting to close this question as off-topic because it belongs on the Avogadro discussion forum. $\endgroup$ Commented Apr 11, 2017 at 18:17


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