[Chimera-users] Measuring distances

[Elaine Meng]

Hi Anindito,
You could pick any specific pair(s) of atoms and measure the distance(s) between them.  However, if you meant that you would like to calculate helix axes and then find the minimum distance between these central axes, that also can be done.

(A) There are several ways to measure the distance between two atoms.  Ctrl-click on first atom, Shift-Ctrl-doubleclick on the second atom and choose "Show Distance" from the resulting context menu is one way.  Or, you could use the "distance" command or the Distances tool (menu: Tools... Structure Analysis...Distances).  See the help for how to use them:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

(B) To calculate helix axes, you would use the Axes/Planes/Centroids tool (in  menu under Tools... Structure Analysis) or the "define axis" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis>

The helix axes will be displayed as cylindrical rods.  Then you can measure the mininum distance between any pair of helix axes by choosing them in the dialog that lists them in a table, or with the "distance" command.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist>

Example commands:
open 1zik
define axis perHelix true #0
distance a1 a2

(the dialog that lists the axes shows they are called a1 and a2)

For distance measurements, axes are treated as finite line segments.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 9, 2022, at 12:59 PM, Eric Pettersen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
>> 
>> From: "Sen, Anindito" <andysen at tamu.edu>
>> Subject: Measuring distances
>> Date: February 9, 2022 at 11:51:15 AM PST
>> To: Chimera-users <chimera-users-bounces at cgl.ucsf.edu>
>> 
>> 
>> Dear All,
>>  
>> How do I measure distances between 2 helices
>>  
>> Stay safe & Regards
>>  
>> Anindito Sen. Ph.D