Hi Daniel, The clip planes are only updated when the graphics is rendered. Unfortunately saving an image doesn't do it. Normally during a script it doesn't draw any graphics unless you explicitly tell it to using the wait command. So you should try hide target m show #1 target ms wait 1 save fig1.png The wait command just means draw the graphics panel of ChimeraX and the arguments says how many frames to draw (often > 1 when recording a movie). I'll see if I can fix ChimeraX so if you save an image in a script it first draws a frame so this trick "wait" won't be needed. Tom

On May 24, 2024, at 1:57 PM, Daniel Asarnow via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Tom/Elaine, I have a series of models with SES surfaces and per-model clipping, and I am trying to create figures for each in a script with several blocks like the following: hide target m show #1 target ms save fig1.png

If I run the commands myself, the figures are as expected, but when I run the script / copy and paste several of these blocks, the surface caps aren't drawn. Am I missing something? Or can I trigger the caps somehow?

Thanks!

Best, -da _______________________________________________ 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/

Awesome, thanks Tom! I actually tried using wait, but I forgot the explicit number of frames was mandatory even for 1. Best, -da On Fri, May 24, 2024 at 4:48 PM Tom Goddard <goddard@sonic.net> wrote:

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I fixed this in the ChimeraX daily build so saving an image in a script will automatically render a graphics frame so updates like clip planes or computing a new volume surface get done before the image is saved. This will not be in 1.8 because we are too close (a few weeks away) to a release.

Tom

...

On May 24, 2024, at 4:26 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Daniel,

The clip planes are only updated when the graphics is rendered. Unfortunately saving an image doesn't do it. Normally during a script it doesn't draw any graphics unless you explicitly tell it to using the wait command. So you should try

hide target m show #1 target ms wait 1 save fig1.png

The wait command just means draw the graphics panel of ChimeraX and the arguments says how many frames to draw (often > 1 when recording a movie). I'll see if I can fix ChimeraX so if you save an image in a script it first draws a frame so this trick "wait" won't be needed.

Tom

...

On May 24, 2024, at 1:57 PM, Daniel Asarnow via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Tom/Elaine, I have a series of models with SES surfaces and per-model clipping, and I am trying to create figures for each in a script with several blocks like the following: hide target m show #1 target ms save fig1.png

If I run the commands myself, the figures are as expected, but when I run the script / copy and paste several of these blocks, the surface caps aren't drawn. Am I missing something? Or can I trigger the caps somehow?

Thanks!

Best, -da _______________________________________________ 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/

_______________________________________________ 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/