Hello Elaine,

I was able to also open a monomer file 1LP3, and the commands (i.e. sym #1 i,222) also worked. I restarted the ChimeraX and opened the molecule again, and it did work this time. But before it stated 'unknown command', in ChimeraX. I am not sure what happened. 

Would it be plausible to create a sphere radius 50 to replicate a 100nm nano-particle as a reference template and then build out the molecule icosahedron using the sym#1 i,222 center x,y,z? 

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student 
Howard University
520-203-1883


On Wed, Jun 5, 2024 at 8:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Heather,
Are you using ChimeraX?  (not Chimera?)  I don't know what you mean by "isn't even recognizing the command," but in ChimeraX 1.7.1 this works fine to make a bunch of copies of 1gcn:

open 1gcn
sym #1 i,222

It's not biologically meaningful for this structure, just using it as a simple example of how the command works.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>

If you want actual atomic copies you would use "copies true" not false, e.g.

sym #1 i,222 copies true

It will not necessarily make a well-packed assembly, you may also need to use the "center" option with an appropriate value for your structure.

Both ChimeraX and Chimera have a Build Structure tool, in case that matters.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 5, 2024, at 5:00 PM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I hope this email finds you well. I have a molecule that I created through the build feature in Chimera, and what I would like to do is just create a sphere of as many copies as it can fit to see the estimated encapsulation volume. However, there is no symmetry assembly to use the matchmaker and I was trying to use the sym command, but it isn't even recognizing the command.
>
> sym #1 i,222
> sym #1 i, n25
> Sym#1 i, 222r
>
> I have tried others with the center command, and I also tried to add copies false NewModel true at the end. What am I plugging in wrong?
>
> The molecule is saved as a pdb, and uploads no issue on ChimeraX.
>
> Thank you,
>
> Heather Noriega
> PhD-Pharmaceutical Science student
> Howard University
> heather.noriega@bison.howard.edu
> 520-203-1883