Bond not displayed in a H2 molecule

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.

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: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Jan 13, 2014, at 11:53 AM, Xavier Andrade xavier@tddft.org 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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Hi Geoff,

I am attaching the file (a few frames of it). The bond dissapears
because I am using the “dynamics bonds” feature.

Thank you,

Xavier

On Tue, Jan 14, 2014 at 9:27 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

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: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Jan 13, 2014, at 11:53 AM, Xavier Andrade xavier@tddft.org 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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Critical Workloads, Development Environments & Everything In Between.
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