[Chimera-users] Distance in pi-interactions

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 3 12:03:02 PDT 2015

Hi George,
That’s right, you cannot show a distance line between centroid objects.

If you want to do that, you have to use a different method to put a fake atom at each centroid, and then measure the distance between the two fake atoms.

The other method is described in this previous post:

You would probably want to delete the centroid objects first, or just start over without centroid objects, so they won’t get in the way.
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 3, 2015, at 11:51 AM, George Tzotzos <gtzotzos at me.com> wrote:
> Hi Elaine,
> It just occurred to me. I used your advice and managed to determine the distance between the two centroids.
> However, I would like to depict it graphically. Having created the two centroids, c1 and c2, I selected them both by Ctrl-click and Shift-Ctrl-click. In the control panel distance c1 c2 gives me the distance as expected. However, I have not manage to generate a distance line by using the Structure Measurements/Distance tool. I think, it’s because it does not recognise the centroids as atoms. I’m attaching a snapshot of this just in case it helps.
> Best regards
> George

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