[Chimera-users] drawing axes of rotational symmetry

Arvind SHARMA arvind.sharma at pasteur.fr
Fri Mar 15 11:12:43 PDT 2019

Hi Elaine,

thanks a lot. Its perfect, exactly what I needed!

Just one more question, is there a way to control the length and width of the rotation axis rod?

best wishes,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, March 15, 2019 5:48:36 PM
To: Arvind SHARMA
Cc: chimera List
Subject: Re: [Chimera-users] drawing axes of rotational symmetry

Hi Arvind,
Here is one approach:

(1) open the structure twice (as two models in Chimera, #0 and #1)

(2) superimpose domain A of one model onto domain B of the other model, using whatever method you prefer (“match” command specifying the exact atoms to use, or “matchmaker” command or GUI which uses CA atoms only and figures out the residue pairing for you, or even by hand, although that is usually harder)


(3) use “measure rotation #0 #1” which will also display an axis (see options for axis color, slab display to show rotation and shift, etc.).  Other things like shift and rotation angle are reported in the Log.

(4) then you could hide or close one copy of the structure since it was only used to figure out this rotation

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

> On Mar 15, 2019, at 8:59 AM, Arvind SHARMA <arvind.sharma at pasteur.fr> wrote:
> Hi,
> I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen?
> Would be great if there is a script available for that and someone can share.
> Have a lovely weekend,
> arvind.

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