Thank you very much for your reply.
Best wishes!
延婷
yanting.tang@mail.nankai.edu.cn
From: Elaine Meng <meng@cgl.ucsf.edu>
Date: 2025-04-29 11:12:49
To: "唐延婷" <1120170412@mail.nankai.edu.cn>
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] How to apply symmetry I to generate an icosahedron model>Hi Yanting,
>Maybe you need to include "copies true" in the "sym" command so that they will be full atomic copies instead of just graphical clones:
>
>sym #2 I,222 center 238.08, 238.08, 238.08 copies true
>
>See explanation of "copies" option:
><https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
>
>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 Apr 28, 2025, at 7:13 PM, 唐延婷 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Hi doctor,
>> when I open a map (ID 1) and a model (ID 2), the map is the whole icosahedron while the model is the protomer of the icosahedron. I want to apply symmetry I to generate an icosahedron model.
>> I have rotated and translated the model into a reasonable position inside the map and then done a “fit in map” to get the initial placement for sym. Then I enter a command ''measure center #1''，center of mass xyz coordinates for map_sharp.mrc = (238.08, 238.08, 238.08)，enter another command ''sym #2 I,222 center 238.08, 238.08, 238.08'' I can see an icosahedron model fit in map.
>> But when I save the icosahedron model.pdb, I found the icosahedron model actually is the model of the protomer.
>> How can I apply symmetry I to generate a true icosahedron model, used for subsequent model refine in coot and real_space_refine in Phenix.
>> Thank you very much. Best wishes!
>> yanting
>>
>> 延婷
>> yanting.tang@mail.nankai.edu.cn
>
>