[Chimera-users] Moving icosahedron to model

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 3 08:46:38 PST 2017

Dear KokLian,
I can’t think of a way to automatically move it to match the symmetry.  However, when you create the icosahedron, if possible you should choose the orientation that is the same as the map data (the colored surface).  Then only translation should be required to match them, so you wouldn’t have to rotate the icosahedron, only move it left-right-up-down.

You can move objects separately with the mouse or with commands.  If you want to save the current position first so that you can return to it if you mess up, use “savepos” (e.g.: savepos p1).  You can return to this position later in the same session with “reset” (e.g.: reset p1).

(A) With the mouse, you have to “freeze” one model and move only the other.  Remember to be careful if you only want to do translation (e.g. middle mouse button or Mac option-touchpad) and not rotation (e.g. left mouse button or touchpad without modifier key).  You can freeze/unfreeze models using the “A” buttons In the Model Panel (open from Favorites menu).

(B) The command to translate is “move” and you can use the “models” option to specify moving only the icosahedron model. You can see which model is which number by looking in the Model Panel (open from Favorites menu).  For example, if the map is #0 and the icosahedron is #1, you could move the icosahedron 10 angstroms to the right with command:

move x 10 mod #1


If you also have to rotate the icosahedron, it can be done with the  mouse and/or the “turn” command, but it may be hard to see what the correct orientation should be.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 3, 2017, at 1:18 AM, KL Ho <hklwork at googlemail.com> wrote:
> Dear All,
> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you.
> Best wishes,
> KokLian
> <image1.png>

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