Hi Heather,
Maybe your other capsid coordinates just happened to be centered on the default location for centering the icosahedron, but this one has offset coordinates.  Still you could just move one or the other (capsid or icosahedron) so that they are centered in the same place. 

In Chimera  (not ChimeraX)  you can deactivate/activate models for motion so that only the active ones move with the mouse.  I.e. uncheck the model number in the "Active models" list under the command line so that only the other one moves with the mouse.  Other ways described here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

I cc'd Chimera-users because the details in this message are about Chimera rather than ChimeraX.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 14, 2022, at 7:06 PM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> Hi Elaine and Tom. I appreciate your help on the inner volume from before both methods with blob and shape, I think I have been able to tailor it for my usage. I also have been using the icosahedron surface in Chimera, and have not had any issues until this capsid, why is it not forming inside the capsid? Did I do something? Thanks in advance.
>  icos_why.py
>
> Thank you,
>
> Heather Noriega
> PhD-Pharmaceutical Science student
> Howard University
> heather.noriega@bison.howard.edu
> 520-203-1883
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