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

[Elaine Meng]

Great!

As a side note, if you use the Actions menu or the toolbar icons, ChimeraX will generate the corresponding command and show it in the Log... so those other approaches might also help in learning commands.

Best,
Elaine

> On Mar 9, 2023, at 3:29 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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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