Dear All,
I am using Avogadro to model hydrogen bond interaction in crystal structure.
I wonder if there is a way to customize hydrogen bond in Avogadro. For
example, intermolecular contacts between C-H***S and N-H***S were found
in crystal structure but these interactions are not recognized in Avagadro.
Although attempt has been made to adjust the hydrogen bond cut-off
radius or angle in the configuration option but the outcome does not
correlate well with expectation.
Besides, what is function of “object” available in the configuration
option? I tried to click on selected atoms and bonds from the drop down
lists but nothing was happen to the molecular structure.
Can anyone please let me know how to do that?
Thank you very much.
Best regards,
Alan
I wonder if there is a way to customize hydrogen bond in Avogadro. For example, intermolecular contacts between C-H∙∙∙S and N-H∙∙∙S were found in crystal structure but these interactions are not recognized in Avagadro.
At the moment, Avogadro only recognizes “classical” hydrogen bonds. Certainly if people have other interactions they’d like to classify, I’m open to broader interpretations.
I think in Avogadro 2.x, we’re also open to the idea of a “zero-order” bond to classify things like coordination to metal centers, agostic interactions, etc. These would largely be manual assignments, but make it nicer for publication-quality images. 
Besides, what is function of “object” available in the configuration option? I tried to click on selected atoms and bonds from the drop down lists but nothing was happen to the molecular structure.
This isn’t so useful for the hydrogen bond engine. But it allows you to hide certain atoms or bonds or to assign some atoms and bonds to particular display types but not others.
Hope that helps,
-Geoff