Here is an example I used ChimeraX to make a movie for the SARS-CoV-2 RNA dependent RNA Polymerase (RdRp). The PDB and EMDB accessions are 6YYT and 11007, respectively.

The ChimeraX scripts are:

open 6yyt
color bychain
open emdb:11007
volume #2 level 2.825
color #2 lightgray
surface dust #2 size 3
hide #1
hide #2
view A1
movie record 
show #1
roll y 1 360
wait 130
hide #1
show #2
wait 50
show #1
wait 50
color zone #2 near #1 dist 5
transparency #2 0
wait 80
hide #1 atoms
cartoon #1
show #1/P,Q,T,U atoms
style #1/T,P,U,Q ball ringfill on
transparency #2 50
wait 120
hide #2
wait 50
view A1
fly 150 A1 A2
wait 150
zoom 2.5 150
wait 150
fly 150 A2 A3
wait 200
movie encode

In the example script, I downloaded PDB and EMDB files by the command “open” and ensure the default display is sphere. Then set the map display with contour level at 2.825, colored in lightgray, dust size 3.

I actually manually select 3 views (use command “view“) to play the transition. Two transitions are shown in the movie. The first one is “fly” and the other one is “zoom“. To be clear, every action designed in the movie must assign frames using “wait“. Otherwise the action will be replaced by the succeeding action immediately. To rotate the object, “roll“, “turn” and “rock” are the commands provided in ChimeraX. They have different ways in rotation, you might want to play it around to figure out the best moving action in your case.

The ChimeraX tutorial is a very useful resource. Highly recommended.