Dear Elaine, Many thanks for this explanation and examples. Does ChimeraX also have the option to symmetrize the cryo-EM 3D maps? If yes - what commands are used for this purpose? Kind regards, Dmitry ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 22 September 2023 16:49 To: Dmitry Semchonok <semchonok@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] symmetrizing the model Hi Dmitry, If you mean to create symmetry copies of an atomic model, it's basically the same command in ChimeraX as in Chimera, "sym", but with some small differences in the options and how you would specify them. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> The easiest case is if the symmetry is already defined in the mmcif structure, e.g.: open 1fav sym #1 assembly 1 ... which by default will create a new model 2 that contains the assembly. There are lots of options, however, including whether it should be a new model or not, so you should look at the help page. If the symmetry is not defined in the mmcif atomic structure file, you can specify symmetry group and parameters directly in the command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry> Example: sym #1 C5 center 0,0,0 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 2:06 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry