[Chimera-users] How to draw 3-fold axis of a Icosahedron

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 17 08:31:28 PDT 2019

There isn’t an option to draw the symmetry axes in this tool.  However, the orientation options in the Icosahedron Surface tool describe which direction it is, for example 

"x 2-fold, z 3-fold (2n3) - with a two-fold symmetry axis of the icosahedron along the x axis and a three-fold symmetry axis along the z axis”


So if you pick the orientation named “2n3", the 3-fold axis is pointing straight at you going in and out of the screen.  You could try creating the axis as a 3D object by making a BILD format file.  For example, if you made a 2n3 icosahedron with radius 100, you could create a text file named something.bild containing something like the following lines and open it in Chimera:

.color yellow
.cylinder 0 0 -100 0 0 +100 5

See BILD format description:

I also attached this as a file named test.bild (just open with “open” command or menu: File…Open).  You can change the color, coordinates (length and direction), and the radius, and also there are other BILD shapes available, such as arrow instead of cylinder.

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

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> On Sep 17, 2019, at 7:24 AM, sunyeping <sunyeping at aliyun.com> wrote:
> Dear everyone,
> I created an icoshedron with  "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw  3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface?
> Thank you in advacne.
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