[chimerax-users] Filled helix tube when clipped

[Elaine Meng]

Hi Zheng,
Sorry, according to my tests, only these surfaces can be shown as solid at the clipping plane:

(1) molecular surfaces
(2) volume isosurfaces (e.g. for density maps)

For the above, it can be controlled with "surface cap true" (or false to turn it off):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap>

I thought it might be possible with the straight cylinders (e.g. shown with "define axis perHelix true" or "shape cylinder") since those are surface models, but I see that they are shown as hollow even if I used "surface cap true" -- tested in the current daily build.

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


> On May 27, 2022, at 1:49 PM, Zheng Ruan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users,
> I'm curious to know if there is a way to have the helix tube filled
> when after using the clip command? I know that the clip plane of
> surface representation can achieve this as found in this example
> (https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png).
> However, I'm not able to make it when I display my structure in
> cartoon cylinder representation. I attached an example image that I
> made.
> Thank you for your input.
> Best,
> Zheng