[chimerax-users] generating icosahedron from pentamer

[Elaine Meng]

Hi Ibrahim,
I don't know what symmetry specification is needed to make one icosahedron from your pentamer.  It depends on the specific coordinates of the pentamer, but is not easy to tell from those coordinates (as you can see).  If #2 is a map of the whole icosahedron, maybe you could try using commands:

measure symmetry #2
...maybe with options, see the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry>

...followed by something like
sym #1 symmetry #2

... with other options, e.g. "center" like you used before, see the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry>

I don't know if this process would work, however; requires that "measure" is able to detect the needed symmetry from the map.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 25, 2021, at 10:03 AM, Moustafa, Ibrahim M. <ria2 at psu.edu> wrote:
> 
> Dear all,
> 
>   I want to generate icosahedral structure from a pentamer (chains A-E). When I use the command:
> 
>    sym #1 i,222 coordinateSystem #2 center #2
> 
>   It generated 5 copies, icosahedron for each chain.
> 
> What I'd like to build is just 12 copies of the pentamer in an icosahedral sym.
> 
>   How to do that in ChimeraX?
> 
> Thanks,
>  Ibrahim
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