Re: [chimerax-users] How to adjust chimeraX's loop display style?
Hi Xiangan, Sorry no, there is no way to smooth the loops (coil) parts of a ribbon or cartoon. Currently only strands can be smoothed.
By "smoothed" I mean that the path of the ribbon may not follow the CA atoms exactly, which can cause problems when the sidechains are displayed.
In Chimera when the sidechains were displayed with ribbon, you could get unrealistically long or short CA-CB bonds.
So in ChimeraX we decided it was more important to have an accurate CA-CB bond length when sidechains are displayed. In the helix and coil (loop) there is no smoothing option so the ribbon is exactly on the CA positions. Strands have a smoothing option turned on by default, because people expect them to be drawn as mostly straight, and if strands are not smoothed, they are very ripply. In ChimeraX when the strands are smoothed but sidechains are shown, the CA atoms that fall off the ribbon are shown with a connecting "tether" instead of stretching or shrinking the CA-CB bond artificially.
This is discussed in the "cartoon" help, see the "smooth" for how to adjust strand smoothing and "cartoon tether": https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether
I investigated whether I could make a smoother representation with the "shape tube" command, but was unsuccessful.
Sorry for the inconvenience -- I'm hoping that explaining the reasons might make it less annoying. :-) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2021, at 1:12 PM, Liu, Xiangan Xiangan.Liu@uth.tmc.edu wrote:
Hi, ChimeraX's default loop style shows very cursive. I like the way loop shows in chimera. Is there any way to make chimeraX's loop display straighter? Thanks, Xiangan
<image.png>
Thank you. I got it.
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 17, 2021 3:39 PM To: Liu, Xiangan Xiangan.Liu@uth.tmc.edu Cc: chimerax@cgl.ucsf.edu chimerax@cgl.ucsf.edu Subject: Re: How to adjust chimeraX's loop display style?
**** EXTERNAL EMAIL ****
Hi Xiangan, Sorry no, there is no way to smooth the loops (coil) parts of a ribbon or cartoon. Currently only strands can be smoothed.
By "smoothed" I mean that the path of the ribbon may not follow the CA atoms exactly, which can cause problems when the sidechains are displayed.
In Chimera when the sidechains were displayed with ribbon, you could get unrealistically long or short CA-CB bonds.
So in ChimeraX we decided it was more important to have an accurate CA-CB bond length when sidechains are displayed. In the helix and coil (loop) there is no smoothing option so the ribbon is exactly on the CA positions. Strands have a smoothing option turned on by default, because people expect them to be drawn as mostly straight, and if strands are not smoothed, they are very ripply. In ChimeraX when the strands are smoothed but sidechains are shown, the CA atoms that fall off the ribbon are shown with a connecting "tether" instead of stretching or shrinking the CA-CB bond artificially.
This is discussed in the "cartoon" help, see the "smooth" for how to adjust strand smoothing and "cartoon tether": <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... > <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... >
I investigated whether I could make a smoother representation with the "shape tube" command, but was unsuccessful.
Sorry for the inconvenience -- I'm hoping that explaining the reasons might make it less annoying. :-) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2021, at 1:12 PM, Liu, Xiangan Xiangan.Liu@uth.tmc.edu wrote:
Hi, ChimeraX's default loop style shows very cursive. I like the way loop shows in chimera. Is there any way to make chimeraX's loop display straighter? Thanks, Xiangan
<image.png>
participants (2)
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Elaine Meng -
Liu, Xiangan