Here is an example of applying MOTIF-EM to the two conformation states of bacteriophage P22.
Create a work-directory containing the two P22 conformations in the form of CryoEM maps: phage-avg-norm.cr0.01.xplor, procapsid-avg-norm.cr0.01.xplor.
Then run MOTIF-EM in the same directory (as per run_commands.html).
Expected run time on a cluster with 100 computing nodes, each about 2Ghz: 1 hour.
Expect results like this.