[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
Tue Sep 17 18:33:27 PDT 2013


Thanks Elaine.

________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Monday, September 16, 2013 1:20 PM
To: Pande, Ajay K
Cc: chimera-users at cgl.ucsf.edu List
Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring

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" <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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