[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
Fri Sep 13 16:23:47 PDT 2013

Hi Ajay,
My previous message already described how to measure the distance between a centroid and an atom. 

There is no angle between two points (centroid and atom), only a line, but you probably meant the angle between such a line and the plane of the Trp or Phe ring.  This is a little trickier and requires one manual calculation.  Steps:

(1) measure the centroid-atom distance, D1 (as described in the previous message)

(2) use Axes/Planes/Centroids to define a plane from the ring atoms

(3) measure the plane-atom distance, D2 (how to do it is the same as measuring the centroid-atom distance except you would choose or specify the plane instead of the centroid)

(4) calculate the angle "manually" as arcsin(D2/D1)

I hope this helps,

On Sep 13, 2013, at 2:50 PM, Pande, Ajay K wrote:

> 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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