[Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 16 10:20:31 PDT 2013

Hi Ajay,
Unfortunately there isn't any way to draw a line between a centroid and an atom.  Instead you would need to add an atom at the centroid position, then measure atom-atom distance (which is shown as a line).

You can add an atom at specified coordinates using Build Structure (in menu under Tools… Structure Editing), Start Structure section.

Centroid coordinates are reported in the Reply Log (under Favorites in menu) when the centroid is created, and can be written to a file using the Save button on the Axes/Planes/Centroids dialog.

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 16, 2013, at 6:44 AM, "Pande, Ajay K" <apande at albany.edu> wrote:

> Thanks Elaine,
> All that worked- thanks. Now, how do I show the line connecting the centroid to an atom (i.e.D1), which would also show its length in Angstroms?
> Thanks
> Ajay

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