[chimerax-users] how to change the radius of loop

[Wen-Jin Winston Wu]

Terrific!
Thanks a lot for your help, Elaine.

Best wishes,

Winston

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Friday, July 2, 2021 10:58 PM
To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw>
Cc: ChimeraX-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] how to change the radius of loop

Hi Winston,
To change the thickness of cartoon loop (= coil, meaning protein non-helix, non-strand), use a command something like

cartoon style coil thickness 0.25

(where 0.25 could be some other number)

"cartoon style" command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

secondary structure specifiers: helix, strand, coil <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin>

As you saw, the "sides" option controls the number of facets in the cross-section.  So if you used "cartoon style sides 8" the ends of the tubes would be in the shape of an octagon.  Higher numbers give a smoother tube because the cross-section gets more like a smooth circle.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 1, 2021, at 11:29 PM, Wen-Jin Winston Wu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Sorry, I have just found the description for sides  N
>  
> sides  N
> The number of straight-line segments used to draw an oval 
> cross-section or the circumference of a tube, with higher numbers 
> corresponding to finer subdivisions (initial default 12). Shading is 
> used to give a smooth, rounded appearance despite this approximation 
> of the shape. See also: graphics quality
>  
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html#hmod
> e
>  
> Best wishes,
> 
> Winston
> 
>  
> From: Wen-Jin Winston Wu [mailto:winston at gate.sinica.edu.tw]
> Sent: Friday, July 2, 2021 2:27 PM
> To: ChimeraX-users at cgl.ucsf.edu
> Subject: how to change the radius of loop
>  
> Hello,
>  
> Does anyone know how to modify the radius of loops?
> I am trying to show structural difference between the three aligned proteins with the cartoon helices shown as tubes.
> However, when I reduced the helix radius from 2 to 1 ( “cartoon style 
> modeh tube rad 1 sides 24”), the radius of a helix is only about twice that of a loop/coil.
>  
> Also, what does the number “24” do in the “sides 24”?. I could not 
> find the description on this on ChimeraX
>  
> Any help will be appreciated.
> Thanks,
>  
> Best wishes,
> 
> Winston