Easily Make a Movie with PyMOL
I realize using the term easy and PyMOL together (at least when dealing with the free version) is somewhat of an oxymoron. So there must be a coveat which is that if you want to make a movie with PyMOL you need to get eMovie. If you haven’t already wasted 6 hours trying to figure out how to make a movie with PyMOL alone feel free to comeback.
Welcome back, so once you have installed eMovie (make to put the files in the correct location as described on the download page) the next step is to start up PyMOL.
If installed correctly you should see an additional GUI (at right) as shown below:
My goal here is to give a basic introduction that will yield a movie that rotates a protein in a full circle. The eMovie website has more advanced examples, but they are not as step by step as shown here.
Usually during a presentation the protein is shown with a white background. This can be done in PyMOL via the PyMOL GUI under Display -> Background -> White
eMovie GUI click Scenes (views, appearances)
Create new scene/Save scene…
name: rotation
click on Rotation in the eMovie GUI (right below Scenes on the GUI)
Axis: y
Degrees: 360
Start Frame: 0
Action Length: 120
-click ok
click Add stop (in GUI)
Insert stop frame: 120
You can now view how the movie looks so far at this point by using the PyMOL GUI click Play (roughly the center button in the GUI)
Tip: save often because if PyMOL or eMovie freeze your settings will be lost (this happens quite frequently).
eMovie GUI click View Storyboard
click on Stop
Deleted selected action
*you must remove the stop before exporting*
eMovie GUI click Export eMovie
(set GUI viewing window to the size of the movie for viewing)
This notice is especially critical if you have different views. You need to make sure that the size of the PyMOL window is consistent. I would recommended making your entire movie in one sitting to avoid a sizing issue.
Tip: If you are going to do multiple views then name them in alphabetical order – in the order in which they appear. For example, you want to do a rotation then zoom – name the rotation frames arotation and bzoom for the zoom (r is before z therefore it would be the right order without the a/b prefix, but hopefully you get the idea).
As a personal preference, I set up a separate folder for each movie which I then export the frames from eMovie into.
Load the rendered images into Adobe ImageReady CS2
File -> Import then select the folder containing the images
You can highlight all the images and adjust the time to 0.1 seconds for smooth playing. Also if you want a delay such as from a rotation to a zoom you can increase the time on that particular frame.
File -> Export original document
Quicktime Movie (may want to consider the type of computer the presentation will be presented on)
Compression settings jpeg -> Best (quality)
Tip: Powerpoint reads the location of the movie files that have been inserted. Therefore you should load the frames on the flash drive with your talk and then save them. This should help avoid the ‘I am not sure why this movie isn’t working’ during your presentation.
Don’t forget to cite PyMOL and eMovie.
admin
March 25th, 2009 at 8:55 PM #
“March 24, 2009: Use of “easy” together with “PyMOL” declared somewhat oxymoronic on the P212121 blog which offers some tips on using the 3rd party eMovie add-on.”
http://pymol.org/
I hope I didn’t offend anyone over at PyMOL with my intro line maybe it is only me that has trouble with PyMOL being intuitive. Nonetheless, I greatly appreciate the time and effort that goes into program development!
Jack
March 29th, 2009 at 2:28 PM #
Thanks for the great tip! Your blog is beginning to look like a valuable resource for a novice crystallographer such as me.
admin
March 29th, 2009 at 2:45 PM #
Hey Jack! Thanks for the comment!
Glad to hear that this maybe a resource to help you out. I don’t have all the answers, but if there are particular concepts/protocols/programs etc.. that you would like to know more about please feel free to leave a reply.
Jacqulyn Pone
April 21st, 2010 at 3:37 AM #
Very interesting post, I truly appreciate you taking the time to place this collectively for visitors like me.