Hello All,

I am experiencing an issue when I am trying to make a movie of a series of coupled atomic models and volumes overlaid on top of each other. I cannot seem to make what I believe is called the "surface cap" transparent when I have clipped into a volume and I am showing/changing the volume. When I call the transparency command in ChimeraX itself (without the script running) it works as it should and makes the surface cap transparent, but in the movie-making script it seems like the transparency command is having no effect? Do you have any suggestions on how to deal with this? Thank you!

Example .cxc code block attempt

clip off; clip near -24.984;
transparency  #1.1 90;

#########################

hide #!*.*;

hide #!* models;

show #!1.2 models;                 #show volume

show #!3 models;                    #show atomic model

transparency #1.2 90;transparency #1.2.1.1 90;

wait 3

hide #!* models;

show #!1.3 models;

show #!4 models;

transparency #1.3 90;transparency #1.3.1.1 90;

wait 3

#########################

Best,

John