Re: [Avogadro-Discuss] Bond not displayed in a H2 molecule

[Geoffrey H. <geo...@gm...>]

The issue would likely be with the underlying Open Babel library. I thought we had a special case for detecting H2, but it's possible there's a bug in bond detection.

Can you send me the file?

I'm also a bit confused why the bond disappears after the first frame when drawn by hand, but I'll investigate.

Thanks very much,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: http://hutchison.chem.pitt.edu/

On Jan 13, 2014, at 11:53 AM, Xavier Andrade <xa...@td...> wrote:

> Hi,
> 
> I am trying to render an animation that involves H2 molecules with
> Avogadro. The problem is that Avogadro is failing to recognize and
> draw the bond between the two hydrogen atoms in the H2 molecules, it
> just draws two isolated H atoms. The atoms are initially set at the
> experimental distance of 0.74 Angstrom.
> 
> Since I need the bonds to change dynamically, drawing the bond by hand
> is not a solution, as it is lost after the first frame.
> 
> Can you suggest me how to solve this problem? Is it possible to
> configure the cutoff distance for bonds or something like that?
> 
> Thank you,
> 
> Xavier
> 
> PS: I am using Avogadro from Debian Sid: Application Version 1.0.3,
> Library Version 1.0.3, Open Babel 2.3.2 and Qt Version: 4.8.6.
> 
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