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
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
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
Hi Tim, I have also many times wished that clipping planes could more easily be reproduced in .cxc files to exactly reproduce a scene. My solution is to first set the window size, then display my reference object, then set the view matrix camera, then unset the clipping planes and then finally set the clip far and near values extracted from a clip list command. This way, I can get pixel-perfect reproduction of a scene. Then I will have to toggle off my reference object and toggle on my map/molecule that I wish to display. Here is an example: 1. Adjust the scene to your liking for a reference object 2. Run the command “view matrix” and copy the camera matrix (first set of 12 comma-separated values) 3. Run the command “clip list” and copy the near and far values 4. Run the command “windowsize” and copy the values When you want to reproduces the scene: 1. Set the window size using the command “windowsize 1000 1000” 2. Hide everything in the scene “hide #!* models” (or “hide #!*.* models” if you load objects hierarchically) 3. Toggle on the reference object using the command “show #!1 models” 4. Set the camera view using “view matrix camera a,b,c,d,e,f,g,h,i,j,k,l” 5. Unset the clip plane using “~clip” 6. Set the clip planes using “clip far m near n” 7. Hide reference object using “hide #!1 models” 8. Show object of interest using “show #!2 models” Where the reference object #1 can be anything, including your actual object of interest. For the record, I tried using the axis and position modifiers to the clip command as was suggested, but I could not get it to work. For example, running clip list, I get this: far offset 72.49, axis 0.555,-0.800,-0.228, point 161.5,253.4,231.2) near offset -124.49, axis -0.555,0.800,0.228, point 270.9,95.91,186.3) Then running these two commands: ~clip clip far 72.49 axis 0.555,-0.800,-0.228 position 161.5,253.4,231.2 clip near -124.49 axis -0.555,0.800,0.228 position 270.9,95.91,186.3 and then clip list again gives me: far offset 144.94, axis 0.555,-0.800,-0.228, point 121.3,311.4,247.7) near offset -248.98, axis -0.555,0.800,0.228, point 340,-3.654,157.9) But if I run these commands, I will get the same clip planes: ~clip clip far 72.49 near -124.49 So, the key to reproducible clip planes is to run ~clip first before setting the clip planes. Regards, Daniel From: Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Reply to: Timothy Springer <springer@crystal.harvard.edu> Date: Sunday, 15 February 2026 at 19:18 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: clip 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<mailto: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<mailto: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
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Daniel and Tim, That recipe for restoring clip planes in a script is so convoluted you have forced me to fix it. In the ChimeraX daily build (dated March 11, 2026 or newer) the "clip list" command will now log the exact command needed to restore each clip plane. clip list Using 1 clip planes: clip front 0 axis -0.969,-0.112,0.221 position 116.5,141.8,155.9 coordinateSystem scene In older ChimeraX (e.g version 1.11) here is how you can make the confusing clip list output reproduce the clip planes. open 8ef5 # Rotate with the mouse clip front -10 clip list Using 1 clip planes: front offset -10, axis 0.980,-0.160,0.121, point on plane 106.7,143.4,154.7) clip off Now to restore this clip plane clip front 0 axis 0.980,-0.160,0.121 position 106.7,143.4,154.7 coordinateSystem #1 Note, the restoring command uses offset 0, not the offset given by "clip list", the axis and position are from clip list, and coordinateSystem #1 is added. (This assumes that you have moved model #1 relative to other models in your scene.) I realize no one would have figured this out. More details about the improved clip list is given in this ChimeraX bug report https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19959 Tom
On Mar 10, 2026, at 8:36 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tim,
I have also many times wished that clipping planes could more easily be reproduced in .cxc files to exactly reproduce a scene. My solution is to first set the window size, then display my reference object, then set the view matrix camera, then unset the clipping planes and then finally set the clip far and near values extracted from a clip list command. This way, I can get pixel-perfect reproduction of a scene. Then I will have to toggle off my reference object and toggle on my map/molecule that I wish to display. Here is an example:
Adjust the scene to your liking for a reference object Run the command “view matrix” and copy the camera matrix (first set of 12 comma-separated values) Run the command “clip list” and copy the near and far values Run the command “windowsize” and copy the values
When you want to reproduces the scene:
Set the window size using the command “windowsize 1000 1000” Hide everything in the scene “hide #!* models” (or “hide #!*.* models” if you load objects hierarchically) Toggle on the reference object using the command “show #!1 models” Set the camera view using “view matrix camera a,b,c,d,e,f,g,h,i,j,k,l” Unset the clip plane using “~clip” Set the clip planes using “clip far m near n” Hide reference object using “hide #!1 models” Show object of interest using “show #!2 models”
Where the reference object #1 can be anything, including your actual object of interest.
For the record, I tried using the axis and position modifiers to the clip command as was suggested, but I could not get it to work. For example, running clip list, I get this:
far offset 72.49, axis 0.555,-0.800,-0.228, point 161.5,253.4,231.2) near offset -124.49, axis -0.555,0.800,0.228, point 270.9,95.91,186.3)
Then running these two commands:
~clip clip far 72.49 axis 0.555,-0.800,-0.228 position 161.5,253.4,231.2 clip near -124.49 axis -0.555,0.800,0.228 position 270.9,95.91,186.3
and then clip list again gives me:
far offset 144.94, axis 0.555,-0.800,-0.228, point 121.3,311.4,247.7) near offset -248.98, axis -0.555,0.800,0.228, point 340,-3.654,157.9)
But if I run these commands, I will get the same clip planes:
~clip clip far 72.49 near -124.49
So, the key to reproducible clip planes is to run ~clip first before setting the clip planes.
Regards, Daniel
From: Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Reply to: Timothy Springer <springer@crystal.harvard.edu <mailto:springer@crystal.harvard.edu>> Date: Sunday, 15 February 2026 at 19:18 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] Re: clip
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 <mailto: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 <mailto: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
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Daniel Larsson -
Elaine Meng -
Timothy Springer -
Tom Goddard