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 heather.noriega@bison.howard.edu 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