Make "clip list" command report exact clip command to restore clipping

[Tom Goddard]

Begin forwarded message:

From: Timothy Springer
Subject: [chimerax-users] Re: clip
Date: February 15, 2026 at 10:17:48 AM PST
To: ChimeraX Users Help

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

[Tom Goddard]

Fixed.

I made the "clip list" command log the clip commands needed to restore the clip planes. For near/far planes the logged clip commands will only restore the correct planes if the camera view direction is the same. For front/back planes the clip planes will restore even if the camera view direction and camera placement is different.

The former "clip list" output was confusing because the axis was reported in scene coordinates but the default axis option of the clip command uses screen coordinates if the coordinateSystem option is not given.

The clip command behavior is also pretty weird in that the axis argument uses screen coordinates if a 3-tuple of numbers is given, but the position argument uses scene coordinates of a 3-tuple of numbers is given, assuming coordinateSystem is not specified. If coordinateSystem is specified than both the axis and position arguments use the specified coordinate if they are given as 3-tuples of numbers.

Here is what the "clip list" output looks like now:

clip list

Using 2 clip planes:
clip front 0 axis -0.963,0.070,-0.259 position 131.7,140.7,160 coordinateSystem scene
clip back 0 axis 0.963,-0.070,0.259 position 112,142.1,154.7 coordinateSystem scene

There is a separate clip command for each plane. In the log these clip commands are executable links.