Introduction and workflow sketch.

Now that you've downloaded eMovie, and hopefully played around with it a little to familiarize yourself with the interface, it's time to make a movie.

Movies range from the simple to the complex, and it can be tough to decide where to start. Below we suggest what we have found to be the best workflow for creating movies using eMovie.

After many of the steps in the workflow you will see a "For example" section. These sections describe how each specific step was performed in the making of Sample Movie 2 entitled "Active site gorge of AChE: Looking down the gorge and zooming in."

1) Preparations
	a. Define what you want to show.	On Paper
	b. Sketch conceptual plot or storyboard.
	c. Translate storyboard into eMovie actions.
	d. Create the morphs (conformation changes or docking actions).	Using PyMOL and eMovie
	e. Create all of the objects and selections (in one session).	In PyMOL (only)
2) Create the scenes		In PyMOL and eMovie
3) Insert actions into eMovie		Using eMovie
4) Review the movie
5) Save the movie

1) Preparations.

1. Define what you want to show (on paper):

The first step, naturally, is to decide on the goal of the movie. What will the movie convey?

For example, "The movie will convey the deepness of acetylcholinesterase's (AChE's) active site gorge."
2. Sketch a rough, conceptual storyboard - the script of the movie (on paper):

This step is purely conceptual, and does not outline specific eMovie actions, but rather describes how the goal of the movie will be met.

For example, "Begin by looking down the deep gorge of AChE presented in a surface representation, rock the molecule back and forth, zoom into the gorge, and rock the molecule back and forth again."
3. Translate the conceptual storyboard into eMovie actions (on paper):

Each conceptual action in the movie's plot must be translated into individual eMovie actions. Make use of scenes (to help change colors, representations, and views), rotations, zooms, and other eMovie actions as necessary. Specific values for the parameters and frame numbers of the actions may be chosen now, but they also may need tweaking as needed later in the movie creation process.

For example, "Rocking AChE back and forth can be accomplished by rotations about y axis: [15°] for 30 frames, [-30°] for 60 frames, and [15°] for 30 frames.
4. Create morph(s) (using eMovie and PyMOL):

It is crucial that any morphs be created before inserting any other objects or actions, otherwise creation of the morph may delete what you have already inserted.

Load into PyMOL the two structures that are to be morphed. Their individual PDB files should have the same chain labelling and the same atom numbering otherwise morphing will not work. Then, use eMovie's 'Make Morph' button to create the morph. eMovie subsequently interacts with PyMOL's RigiMOL morphing module to produce a sequence of states with interpolated atom position changes which ,when viewed in sequential order, or reverse order, looks like a morphing from one structure to the other.

Note: the subscription version of PyMOL, incentive PyMOL (iPyMOL), is required for the creation of morphs, because only this version includes the morphing module RigiMOL. Also, make sure you have downloaded eMovie_rigimol.inp in addition to eMovie.py from the download page.
5. Create all the objects and selections (in PyMOL only, in one PyMOL session):

One, all-inclusive PyMOL session should contain each object and selection to be used in the movie. One will have to decide which objects and selections are necessary for the movie, and create them (in some situations, even duplicate objects of the same molecule can be useful).

For example, "Load 1ea5.pdb, a file containing the crystal structure of AChE, into PyMOL. Then create different selections within the protein such as: separate selection for the residues that make up the active site gorge, another one for the catalytic triad."

2) Create the scenes.

The more complex the movie, the more scenes it will likely contain. Scenes can store specific representations of objects, their colors, and the camera view. Each distinct combination of representations, colors, and camera view should now be stored as a separate scene such as the initial and the final scenes and others.

Use PyMOL to define the combination for the particular scene. Then use eMovie to save the scene - click on 'Scenes (views, appearances)' button and then click on 'Create Scene' button and give the new scene a name and save it.

For example, "To store the initial scene, first choose the representations, colors, and view: set the AChE object to display in surface representation. color AChE green, color the residues in the gorge white, and color the catalytic triad red, and set the view to look directly into the AChE active site gorge. Now save the scene as 'first_scene'."

3) Insert the sequence of actions into eMovie.

First insert the morphs using 'Add Morph to eMovie', and then insert the rest of the individual eMovie actions.

Perhaps the most logical way to insert the individual eMovie actions is in chronological order, although the actions can be inserted in an order not corresponding to their order in the actual movie. Setting the initial scene first seems to make sense, but, again, the initial scene does not have to be the first action inserted.

Use the 'Scenes (views, appearances)' button and then 'Insert Scene' to insert an already created scene into the desired frame. Use eMovie's buttons to add the other actions (e.g. rotations, zooms, fadings).

For example, "Enter the name of our initial scene, 'first_scene', and specify to insert that scene at frame 1."

Note: when the movie plays and encounters a scene change, the scene change takes time to load, therefore you should always allow at least about 20 to 50 frames with no action after a scene setting action in a movie (depending on the speed of the computer). If, as the movie is playing, there is not sufficient time for a scene to load before the next action (e.g. a rotation) begins, the scene may not finish loading and the view and the pace of the movie may be thrown off.

4) Review the movie and make adjustments.

Now that the movie is complete, review the movie by playing it in PyMOL.

The 'Scenes (views, appearances)' button may be used to view each individual scene. The 'View Storyboard' button may be used to view and edit the individual actions that make up the movie.

5) Save the movie.

Use 'Save eMovie', while making the movie, to save the movie occasionally so as to reduce the risk of accidentally losing your movie. Save the final version when you finish.

To save the movie in a traditional movie format (like .mov, .gif or .mpeg) there are two basic options:

• Use the 'Export eMovie' button - This exports the movie as a sequence of image files (.png) with the option of ray-tracing each image. The image sequence can then be combined to form a movie in the traditional format (e.g. .mov, .gif, or .mpeg) by using mencoder (Unix, Windows), Graphic Converter (Mac OS X), Movie Maker (Windows), VideoMach (Windows), Adobe Premiere (Windows), Berkeley encode_mpeg (Unix/Linux), or other, similar programs.

• Mac users have what may perhaps be called a simpler option: After creating the movie using eMovie in PyMOLX11Hybrid, and saving it using eMovie, the final movie may then also be saved using the PyMOL 'File/Save Session' feature. The saved session file (.pse) may then be opened in MacPyMOL (not PyMOLX11Hybrid), and exported using MacPyMOL's unique 'File/Save Movie/QuickTime' feature.

After the movie is in a traditional movie format, you can add titles, voice-over, music, labels, and end credits using other programs.

Please send us movies you've made using eMovie! We would love to display them on this website.

And don't forget to cite eMovie!