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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
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