To record a movie showing grayscale planes of a 3D electron microscopy map use the planes option of the volume command. To put a numeric label giving the plane number on each frame of the video we use the 2dlabel command. To cycle through the planes and update the labels we use the perframe command that runs the needed volume and 2dlabel commands once for each plane to be shown.
Normally I load the data and set the thresholds and zooming using the ChimeraX graphical user interface and then save it as a session in case I want to change the movie in the future. But here I’ll show commands that do the setup for completeness. I use orthographic camera mode instead of the default perspective mode so that the planes don’t change size with distance.
windowsize 500 500 open 22910 from emdb volume #1 style image level -0.4458,0 level 2.326,1 plane z,100 view orient zoom 2 camera ortho 2dlabel text "plane number" xpos 0.8 ypos 0.1
Then use the movie command to record the movie.
movie record size 500,500 perframe "volume #1 plane z,$1 ; 2dlabel #2.1 text $1" range 100,300 wait 201 movie encode ~/Desktop/planes.mp4 quality high
Tom Goddard, April 22, 2021