Hi Tim,

  ChimeraX sessions remember the ChimeraX window size but they don't restore it by default because we think most people prefer the ChimeraX window to stay at the size they were using when they previously ran ChimeraX or the size they created with the mouse.  But there is an option in ChimeraX / Settings (under the UCSF ChimeraX menu on Mac, or under the Favorites menu on Windows and Linux) called "Resize graphics window on session restore" that will set the ChimeraX window size whenever you open a session to the size it had when the session was saved.  This can be useful if you are trying to modify a previously made image and want the exact same aspect ratio.

  I see that ChimeraX Scene documentation says that window size is saved.  But it is not restored by default.  And there is another option "Reize graphics window on scene restore" in the same place as the option to resize for session restore.  We will add that to the scene documentation.

Tom
windowsize.png
On Aug 10, 2026, at 5:56 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks, I had the daily build and updated to 1.12. 
I am now using .cxs files. The scenes command did not restore my window size? If that is not implemented, let me know what to do. 


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


On Wed, Aug 5, 2026 at 6:11 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Tim,

  Are you using the current ChimeraX version 1.12?  It is supposed to report the exact clip command to restore the clip planes.  This improvement to the clip list command resulted from your February mailing list message, but perhaps you missed the reply in the mailing list saying it was changed based on your request


If you are using ChimeraX 1.12 and it still is not working use menu entry Help / Report a Bug so I can look at what the problem is.

  I did not change the windowsize output to log the exact command used to restore the window size.  The purpose of the ChimeraX Log is primarily to report information to a human user in a clear way, usually that is not in the form of commands that tend to be harder to read.  You are perhaps accustomed to copying and pasting lots of commands from PyMol, but that is not the usual workflow in ChimeraX.  For the clip command it made sense to Log the command since there are few other reasons for the user to ask about clip parameters.  But for the windowsize command probably most users are just checking the size, not trying to copy the command.  For instance you might use to see if the image size meets journal publication requirements.

  Unfortunately Elaine retired a month ago.  But the UCSF ChimeraX team carries on.

Tom


On Aug 5, 2026, at 2:24 PM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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

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