Hello, I do not want to save the shape of a sphere. I was using that for something else while creating the nano. Ok, that is what I did wrong. I did not include the copies true command. I have a question. I used the commands: Sym #1 i,2n3 center 20,20,20 and Sym #1 2n5 center 20,20,20 to create the sphere. Would I have to add copies true to both commands? sym#1 i,2n3 center 20,20,20 copies true sym#1 i,2n5 center 20,20,20 copies true And then continue with the saving process for PDB Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 On Fri, Jun 21, 2024 at 12:37 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Heather, I can't tell what you are trying to save exactly but here are two issues:
(1) when you used "sym" the Log said it was making graphical clones. (The log contents are included in the session file.) If you want full atomic copies instead of graphical clones you have to use "copies true" as explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
(2) The big sphere seems to be a surface model, and you can't save a surface model as PDB format. Maybe you used the "shape" command, which creates surface models. But I can't tell from your message whether you are trying to save that in the file or not.
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 21, 2024, at 9:16 AM, Noriega, Heather via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether?
I attached the session below for your reference.
Thanks, Happy Friday!
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 <nano_span_60.cxs>