[Chimera-users] Distance in pi-interactions

George Tzotzos gtzotzos at me.com
Thu Sep 3 11:51:25 PDT 2015

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


> On 03 Sep 2015, at 18:40, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi George,
> You can define a centroid for each ring and then measure the centroid-centroid distance.  This could be done with the Axes/Planes/Centroids graphical interface (in menu under Tools… Structure Analysis) or with the commands “define” and “distance”.
> With the graphical tool you’d click the “Define centroid…” button.  You’d need to select the first set of atoms in the main window (the usual way, Ctrl-click the first, Shift-Ctrl-click  to keep adding more atoms to the selection) before apply/OK..  Then you’d need to select the second set of atoms and define centroid again.  Then the dialog will list two centroids, and you can just choose both rows with the mouse to have the distance reported near the bottom of that same dialog.  Details:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> With “define centroid” you’d have to either select the atoms and use “sel” or specify them directly by residue number and atom names, and you’d need to use “define" twice to define the two different centroids.  Then you could use the “distance” command with the IDs of the two centroids.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> I hope this helps,
> Elaine
> ----------
> 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 7:53 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> I’m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I’m attaching a snapshot for easy reference.
>> Thanks in advance for any suggestions.
>> Regards
>> George

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