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
Sorry, I have just found the description for sides N sides N The number of straight-line segments used to draw an <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html#xsection> oval cross-section or the circumference of a <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html#hmode> 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: <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> graphics quality https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html#hmode Best wishes, Winston From: Wen-Jin Winston Wu [mailto:winston@gate.sinica.edu.tw] Sent: Friday, July 2, 2021 2:27 PM To: ChimeraX-users@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
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@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#hmode
Best wishes,
Winston
From: Wen-Jin Winston Wu [mailto:winston@gate.sinica.edu.tw] Sent: Friday, July 2, 2021 2:27 PM To: ChimeraX-users@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
Terrific! Thanks a lot for your help, Elaine. Best wishes, Winston -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 2, 2021 10:58 PM To: Wen-Jin Winston Wu <winston@gate.sinica.edu.tw> Cc: ChimeraX-users@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@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@gate.sinica.edu.tw] Sent: Friday, July 2, 2021 2:27 PM To: ChimeraX-users@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
participants (2)
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Elaine Meng -
Wen-Jin Winston Wu