Hello, That is ok. I appreciate your honesty and do appreciate the guidance. Heather On Wed, Jun 5, 2024, 9:54 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
I can't really comment on plausibility for your research project. It's beyond the scope of this mailing list, which is mainly for discussing how/whether you can perform some relatively specific task with our software.
All I can say is that sym will generate rigid copies of the structure according to the symmetry that you give, but they may pack poorly with either a lot of void space, or a lot of intersections, or both. You have to just look at it and judge for yourself whether it is good enough for your purposes.
There may be other software that more carefully packs copies of your structure (CellPack?? <https://www.nature.com/articles/nmeth.3204>)
...but I don't know and I have not used such software myself, so I can't provide any more details. Sorry about that,
Elaine
On Jun 5, 2024, at 6:29 PM, Noriega, Heather via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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
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