I appreciate you for your help! After reading the e-mail I wrote to you, I found my question was not that specific and too ambiguous. But you've catched my demands and answered with great effort. I apologize and thank you again for your answer! Have a nice day. 🙂 Best regards, Gumin Han ________________________________ 보낸 사람: Elaine Meng <meng@cgl.ucsf.edu> 보낸 날짜: 2026년 1월 8일 목요일 오전 12:18 받는 사람: 한구민(생명과학과) <naeshi9min@postech.ac.kr> 참조: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> 제목: Re: [chimerax-users] Surface overlapping with atomic model Hi Gumin Han! This figure is showing both the molecular surface and the ribbons of the same structure, with the molecular surface transparent. Some atoms/bonds are also shown as sticks. Probably this figure was not made in ChimeraX, but you could do something similar. In ChimeraX, you can just - open the structure, show as ribbons - also show some atoms if you want - show molecular surface and make it transparent - color patches of the molecular surface differently if you want Example commands (you could also use menus but easier/shorter for me to show commands in this email): open 4hhb preset Publication 1 surface transparency 75 color ligand :<5 green target s However, this still looks different in detail than your example image, which does not have shading or outlines on the surface part. In ChimeraX you can try this command to remove some but not all shading: lighting flat However, I cannot think of any command to remove the outlines on the surface but keep them on the ribbons/atoms at the same time. Instead you may have to save two separate image files from ChimeraX, one with no surface and outlines turned on, ~surf ... and another with surface only and outlines turned off, surf hide ribbons hide atoms graphics silhouettes false ....and then use some other program outside of ChimeraX (like Gimp or Photoshop) to put the two images together. However, even then it would not be exactly the same as the figure you referenced, because there would still be some shading on the surface in ChimeraX. Please see the ChimeraX help pages for the details of each command and its options. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> 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 Jan 6, 2026, at 9:23 PM, naeshi9min--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I'm Gumin Han from South Korea.

Thank you for your wonderful visualization tools. This is my first time writing a question here. I want to overlap my models with surface as shown in the link (Figure panel B) https://www.nature.com/articles/s41467-024-49516-2/figures/1

Which options should I use?

Thank you for reading my E-mail and best wishes for the New Year' Best regards, 2026, Jan 7th Gumin Han _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/