Hi Elaine, Thanks for your excellent support. As I understand, only view spec saves the clipping planes. Otherwise they are default based on the objects in the view. I want to carefully adjust the planes, which is not possible with view alone. Scenes saves clipping planes, but only in sessions.
Pymol does save clipping planes in views, and it copies the exact command to the log file, which is a nice feature for use in .pml files. Pymol has more examples of each command. You did point me to read the usage lines in the command help page, but these are still difficult for me to understand. 
Pymol is easier for people who want command line control. Chimerax has a better gui and most people use the gui. It also has wonderful command line features. I wish the log files would echo the exact command needed to reproduce something, but there is often a change in syntax as in the clip commands. I notice this in windowsize, too. when the window size is reported, it is window size x, y. why not make it windowsize x, y so one can copy directly to a .cxc file? Why not make the clip list command print out exactly what is needed in a command line?

- Tim
Timothy A. Springer, Ph.D.
Latham Family Professor, Harvard Medical School and Boston Children's Hospital
Founder, Institute for Protein Innovation


On Fri, Feb 13, 2026 at 12:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Tim,
You can certainly use "clip list" in a cxc file.

If you mean you want to set the clipping planes the same as reported by "clip list" you might want to consider using "view" instead.  I.e. If there is a specific scene (specific molecules in specific orientations) being clipped, one would generally save  a named view, which includes the clipping plane positions, and then restore the view later as needed (see "view" command for both saving and restoring), and save a session (.cxs file) which includes all your named views.

However, you could certainly try using "clip" to set the near and far clipping planes with the same offset, axis, position as reported.  See the usage of the "clip" command, practically the same as what you get from back from "clip list":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

Example
clip near -3.0783 axis  -0.462,-0.880,0.109 position 218.1,184.5,202.4

How to read the usage lines in command help pages:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html>

I hope this helps,
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 Feb 13, 2026, at 8:00 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Can you translate this into a clip command I can use in a .cxc file?
> clip list
> Using 2 clip planes:
> near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4)
> far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1)
>
> - Tim
> Timothy A. Springer, Ph.D.
> Latham Family Professor, Harvard Medical School and Boston Children's Hospital
> Founder, Institute for Protein Innovation