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

Pande, Ajay K apande at albany.edu
Fri Sep 13 14:50:49 PDT 2013


Hi Elaine

Thanks for the information. But if I want the angle (and distance) from the centroid of a ring system (Trp or Phe , for example) to the SG of a Cys, how would I get that?

Ajay


________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 12, 2013 7:52 PM
To: Pande, Ajay K
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring

Hi Ajay,
I'm not sure how (or why) you are trying to draw an axis between an atom and a centroid: an axis is calculated from a set of atoms and it won't work to generate an axis from one atom and one centroid.

If you are just trying to measure the distance, you only need  select the SG atom (for example using Ctrl-click) and then click on the row for the centroid in the Axes/Planes/Centroids table and then the "Report distance" button in the same dialog.  It will show the distance on the dialog and in the Reply Log.  Or, you could use the "distance" command, for example between centroid with ID c1 (as shown in the table) and atom SG in Cys-25 of model 0 chain A:

distance c1 #0:25.a at sg

This will report the distance in the status line across the bottom of the Chimera window and in the reply log.
<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 12, 2013, at 1:52 PM, "Pande, Ajay K" <apande at albany.edu> wrote:

> I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.






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