Recalculating the bonds

General Discussion
1

Dear List,

I just started using Avogadro (0.9.4), so a very basic question…

After moving atoms in my molecular structure, how can I
recalculate the bonds?

… i.e. if I have atoms 1,2,3 and
originally the bond is between 1 and 2, but then I move
the atoms so that the bond should now show between atoms 2 and 3.
… but avogadro does not seem to do this.

Regards,

Sampsa

2

I just started using Avogadro (0.9.4), so a very basic question.

First off, I’d suggest trying v. 1.0. It’s much better. :slight_smile:

After moving atoms in my molecular structure, how can I
recalculate the bonds?

At the moment, there is no “rebond” command. However, you can draw new bonds and delete existing ones manually.

To delete a bond:

  • Using the draw tool, right click in the middle of the bond

To draw a new bond:

  • Using the draw tool, select the bond order you want (e.g., single, double, triple) and drag between the two atoms. A new bond is created.

Hope that helps,
-Geoff

3

On Friday 11 December 2009 10:02:53 pm Geoffrey Hutchison wrote:

I just started using Avogadro (0.9.4), so a very basic question.

First off, I’d suggest trying v. 1.0. It’s much better. :slight_smile:

After moving atoms in my molecular structure, how can I
recalculate the bonds?

At the moment, there is no “rebond” command. However, you can draw new
bonds and delete existing ones manually.

Hello,

And thank you for your replies. … the “rebond” command was exactly
what I was looking for. I mean, if the program knows how to calculate
the bonds, then why one can’t make it to repeat this procedure…
… is there any way to do this from the python console?

Regards,

Sampsa

To delete a bond:

  • Using the draw tool, right click in the middle of the bond

To draw a new bond:

  • Using the draw tool, select the bond order you want (e.g., single,
    double, triple) and drag between the two atoms. A new bond is created.

Hope that helps,
-Geoff