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

Tom Goddard goddard at sonic.net
Mon Sep 16 10:43:24 PDT 2013


Another way to mark the center of a ring is with the command "measure center".  After selecting the ring atoms use

	measure center sel mark true radius 0.5

This places a marker (same as an atom) at the center and makes its radius 0.5.  Then use that marker/atom to show and measure distance.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center

  Tom


On Sep 16, 2013, at 10:20 AM, Elaine Meng > wrote:
 
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
> 
> 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.
> 
> Best
> 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 16, 2013, at 6:44 AM, "Pande, Ajay K" 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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