Re: [chimerax-users] Showing atoms of select residues while also showing the remainder of the model

Thanks Elaine, I used your solution B with the command line. It work as I was hoping. BTW: I am liking the command line approach more and more. That way I better learn what Chimerax has to offer by doing that. Phil ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, March 9, 2023 5:25 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Showing atoms of select residues while also showing the remainder of the model Hi Phil, (A) Instead of command: show target a You could use command: show sel target a See the command help, where the "spec" shown in the usage can be several different things including the word "sel" to mean the current selection: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html> (B) Alternatively, you could skip making the selection (your step 2) and specify the atoms directly in the show command: show /A:102,105,106 target a If you click the "spec" link in the command help, it goes to this other page describing the different ways to specify atoms, models, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> (C) yet other ways of acting on the current selection would be to - click icons in the toolbar across the top, e.g. the "show atoms" icon that looks like phenylalanine sidechain sticks <https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html> - use the Actions menu, e.g. Actions... Atoms/Bonds... Show <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 9, 2023, at 2:51 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Everyone,

I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did:

1. Opened the model from my working directory 2. Selected a subset of residues using the select command: sel /A:102,105,106 3. Then used this command: show target a

This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format.

Thanks for any advice.

Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users