These are some notes while using PyMOL

• From file choose open and choose your pdb file

• From file choose open and choose the different pdbs you want
• From plugin choose Alignmentchoose Many to one

• At the right pane you should see the name of the pdb file, click on H that refers to hide, then click on water

• From the upper toolbox, From scene choose from Append --> Camera
• From the upper toolbox, From Movie choose from program > camera loop > Nutate and any time frame you want, you can also choose anything other than Nutate or camera loop
• Lastly click on play from the upper right pane or the play icon in the lower right pane
• To save this video, From file choose export movie as choose MPEG choose save movie as write the name you want and wait until it's exported