Thank you Elaine, clip list is the function I am looking for, so that I can set the clip plan to see. Thanks! Hong

On Jul 31, 2022, at 11:33 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Hong, You can control clipping with the "clip" command. If you first interactively set up clipping in the positions that you want and then use command "clip list", it will report positions in the Log, which may help you figure out what option values to use in your script with the "clip" command.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

Another command that sets clipping is "view" e.g.

open 2gbp view ligand

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>

If you mean you want the Side View GUI shown in the ChimeraX window, you can start it with command:

tool show "Side View"

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html>

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 31, 2022, at 8:38 AM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all, I would like to setup a movie sequence using cxc file. It is very useful to setup in the UI window, however, any tricks could I use to set the clip plane in the command line to generate a view as in the attached picture? So that I can run my cxc file together with other actions? Many thanks! Hong

<Screen Shot 2022-07-31 at 10.37.10 AM.png>