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Thanks Elaine,</div>
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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.</div>
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Phil</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, March 9, 2023 5:25 PM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Showing atoms of select residues while also showing the remainder of the model</font>
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<div class="PlainText">Hi Phil,<br>
(A) Instead of command: <br>
<br>
show target a<br>
<br>
You could use command: <br>
<br>
show sel target a<br>
<br>
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:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html</a>><br>
<br>
(B) Alternatively, you could skip making the selection (your step 2) and specify the atoms directly in the show command:<br>
<br>
show /A:102,105,106 target a<br>
<br>
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.<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html</a>><br>
<br>
(C) yet other ways of acting on the current selection would be to<br>
<br>
- click icons in the toolbar across the top, e.g. the "show atoms" icon that looks like phenylalanine sidechain sticks<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html</a>><br>
<br>
- use the Actions menu, e.g. Actions... Atoms/Bonds... Show<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions">https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 9, 2023, at 2:51 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Everyone,<br>
> <br>
> 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:<br>
> <br>
> 1. Opened the model from my working directory <br>
> 2. Selected a subset of residues using the select command: sel /A:102,105,106<br>
> 3. Then used this command: show target a<br>
> <br>
> 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.<br>
> <br>
> Thanks for any advice.<br>
> <br>
> Phil McClean<br>
> _______________________________________________<br>
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