Question about Avogadro bonds display

General Discussion
1

hello,

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Thanks!

2

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Good question. At the moment, no. I see that you’re using a @me.com address. If you’d like this, I can code it up in a few minutes and add it to the nightly Mac build tonight?

http://avogadro.openmolecules.net/nightly/mac/unstable/

-Geoff

3

You’re right, I forgot to say I am using it on Mac OS. Thanks, I can give a try to the nightly build.

By the way, I came up with temporary solution. It is a general solution than can even be extended to Periodic systems like Slabs.

To illustrate the trick with an example, let’s say we have a slab of a metal with an organic molecule over the surface. If we were to remove to bonds within the slab ( not the molecule), a possible solution could be:

  1. Create a display type only for the organic molecule, removing the slab part.
  2. Create a second display type only the slab part.
  3. When showing only the second display type, select by element in order to select all metallic atoms.
  4. Invert the selection. This will select only bonds
  5. Removing them.
  6. Showing back first and second display type (now with no bonds in this second), we would have the whole system without the bonds.

It’s not a bad trick. The key is to isolate in a display type atoms whose bonds are to be removed. The only caveat is that bonds are removed instead of just hidden, but that’s a matter of backing up the file before editing.

Hope this helps :slight_smile:

I am starting to use Avogadro latest version 1.1.0 . I am working with a cluster system. Is there a way to only display atoms and hide all bonds? Without manually removing each of them.

Good question. At the moment, no. I see that you’re using a @me.com address. If you’d like this, I can code it up in a few minutes and add it to the nightly Mac build tonight?

Avogadro Nightly Build: Unstable

-Geoff