I guess another possibility is to open the structure twice and use one copy for the ribbon and the other for the (selected) sidechain atoms.  However, that might be a pain!

Elaine

> On Oct 3, 2024, at 8:58 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi James,
> That is simply how selecting works:  if you have even one atom selected it will also mark the residue containing that atom as selected, and hence draw a selection outline around the ribbon segment of that residue.  Selection was meant to be an operational tool (it would still be possible to act only on the atom and not the ribbon), not a way of drawing a specific outline for a figure, sorry.
>
> Maybe there is some other way you can emphasize the sidechain, like making it fatter or a different color?   Otherwise if you only want an outline on the atoms but with a transparent ribbon you may need to composite two images, or add the outline in some image-editing program like Gimp or Photoshop.
>
> I hope this clarifies the situation,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Oct 2, 2024, at 11:31 PM, James Lingford via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Dear ChimeraX team,
>>
>> I want to select only the sidechains of a protein in order to visually outline them for a figure. This isn't an issue if cartoons are turned off, because I can select the only sidechains I want and use the command:
>>
>> `sel sel & sidechain`
>> and I outline them in a nice way with...
>> `graphics sel col black width 2`
>>
>> However, if cartoons are turned on then this won't select just the sidechain, but select a portion of the cartoon backbone too. I'm not sure how to specify this.
>>
>> Ideally I want a transparent cartoon with opaque sidechains, and then have only the sidechains selected. Please see the images attached for examples of what I'm referring to.
>>
>> Many thanks,
>> James
>
>
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