How to apply symmetry I to generate an icosahedron model
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
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
Dear Elaine Meng, 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
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Elaine Meng -
唐延婷