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

[McClean, Phillip]

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 at cgl.ucsf.edu>
Sent: Thursday, March 9, 2023 5:25 PM
To: McClean, Phillip <phillip.mcclean at ndsu.edu>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at 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 at 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
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