Thanks Elaine! It works! Best, Jiaxuan From: Elaine Meng <meng@cgl.ucsf.edu> Date: Sunday, May 14, 2023 at 12:24 PM To: Cheng, Jiaxuan (NIH/VRC) [F] <jiaxuan.cheng@nih.gov> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Measuring distance between two atoms in a single protein Hi Jiaxuan, I don't know where you are looking that suggests you can use "at" -- instead to indicate atom name it is the @ symbol. The command would instead be something like distance #1.16/B:94@CA #1.35/B:94@CA How to write atom-specs in the command line is described in this page: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fatomspec.html&data=05%7C01%7Cjiaxuan.cheng%40nih.gov%7C30c1708112bc4941f25e08db5497ac53%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638196782642531483%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=om6G40SkXMocuH5HWsY5YPtMA0oOc5oLeC8FCxsLyl8%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 12, 2023, at 9:19 PM, Cheng, Jiaxuan (NIH/VRC) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Elaine,

I met a problem when measuring the distance between two atoms. I entered “distance #1.16/B:94 at CA #1.35/B:94 at CA” , but the ChimeraX reports “expected a keyword”. Could you let me know how to solve it?

Thanks! Jiaxuan

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