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.