[Chimera-users] measuring distance between an atom and centroid of an aromatic ring

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 8 17:12:11 PDT 2014


Hello Aswani,
It won’t draw a line like atom-atom distance measurements, but you can certainly get the values.  You can use the distance command to get a pairwise centroid-atom distance, for example:

distance c1 #0:200.A at n

(centroid with ID c1 to atom N in residue 200 chain A of model 0).  The centroid IDs are shown in the Axes/Planes/Centroids dialog.

Or, you could select one atom and use command:

distance c1 sel

Or, to measure the distances from a centroid to multiple selected atoms, choose the row for the centroid in the Axes/Planes/Centroids dialog and then click the “Report distance” button.

In all cases, the resulting distance values will be reported in the Reply Log (main menu Favorites… Reply Log).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

The centroid is actually a surface model and not an atom, which is why the behavior is different than with two atoms.  If you wanted to make a fake atom in the centroid position, it is a bit more bothersome.  To do that, you could use the “Save” button on Axes/Planes/Centroids to save the centroids information including their coordinates to a text file.  Then you could use Build Structure (in menu under Tools… Structure Editing), “Start Structure” and Add: “atom” with specified x,y,z coordinates copied from that file.  Then after you added the fake atom, you could use it for distance measurements the usual atom-atom way.

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 Oct 8, 2014, at 4:03 PM, Aswani Kumar Kancherla <ashwin2952 at gmail.com> wrote:

> Hello Chimera Users,
> 
> I need to measure and mark the distances of a few atoms to the center of an aromatic ring. 
> 
> I could define and create a centroid and plane for the ring. However, I am unable to measure or mark the distances of the surrounding atoms from the centroid of the ring (This is an exercise to show the ring current effect of the aromatic ring on the chemical shifts of the neighboring protons). 
> 
> Could anyone please give a hint on how I can go about this?
> 
> thanking you in advance,
> best wishes,
> Aswani




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