Hi Elaine,

The clip command does not work for me. When i copy from clip list, and translate into the command line, the clipping plane moves instead of remaining where it was as reported by list. I wonder if it is interpreting as a movement amount from the camera, rather than an absolute position from the camera.

So adding these to .cxc file seems useless to me.

I am using .cxc file and view and scenes appear to require .cxs files.

Can I complain? Pymol reports values just as they would be needed to put in commands, and clip list is very far from that. Even windowsize differs, it returns window size x y which needs translation to windowsize x y if used as a command.

Can ChimeraX developers try to achieve this uniformity?

Some of my colleagues save values in other files and input them into .cxs files. Would it be easier for me to join that crowd and start using .cxs? Seems chimera is oriented to .cxs.

- 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