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

[Elaine Meng]

Hi,
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”

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosahedron.html>

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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>

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
-----
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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