Clickable eMovie menu bar with short descriptions of each button.

More detailed explanations of the eMovie buttons further down the page.

Clickable eMovie menu bar	Short button descriptions
	Manage PyMOL scenes: create, recall, delete, and insert scenes.
	Insert a rotation.
	Insert either a zooming in or out action.
	Insert a PyMOL command to be executed at a specified frame during the movie.
	Fade in or out a molecule/selection.
	Insert a dynamic Cα backbone trace of a protein.
	Insert a pause into the movie, which is often most useful at the end of movies.
	Insert a stop at a specific point in the movie. (Good for presentations.)
	Create a morph between two molecules. (Requires iPyMOL.)
	Insert a morph into the movie.
	Load a morph from a file into the movie for later insertion.
	View/edit the current list of actions comprising the movie.
	Save the current movie.
	Load a previously saved movie (that was created using eMovie).
	Export the eMovie as a sequence of numbered images (.png).

Detailed description of the eMovie menu bar buttons.

Action in all movies made with eMovie is divided into single pictures called frames. In many cases, inserting an action into the movie requires the user to specify a start frame and an action length. The start frame is simply the frame at which the action should begin, and the action length is the frame range over which the action should take place.

Scenes (views, appearances)

eMovie uses PyMOL scenes to handle dynamic view, color, and representation changes. This button is used to manage PyMOL scenes, including creating new scenes, recalling existing scenes, deleting scenes, and inserting scenes into the movie. In creating a new scene, the user gives a name to the new scene and specifies whether it should save the current coloring, representations, and/or view. (figure)

Rotation

Insertion of camera angle rotations of a specified degree and axis into the movie. Rotation speed can be controlled by varying the action length parameter. Only the x, y, or z axis can be specified, but combinations of the three can be added by creating more than one rotation action over the same frame range. (figure)

Zoom

Insertion of either a zooming in or a zooming out action into the movie. The amount of zoom is specified in angstroms and will be a 'zoom out' if a negative number is given. (figure)

Add Command

Insertion of a PyMOL command to be executed at a specified frame. The command can be anything from a one-line command to an execution of an external script. This allows eMovie to incorporate into the movie any actions or commands that are not available through the eMovie GUI, thus greatly enhancing the flexibility of eMovie. (figure)

Fading

Fading in or fading out of a molecule/selection. The molecule to be faded in or out must be shown either as stick, surface, cartoon, or sphere representation, and the user specifies which of these representations will undergo fading. It is even possible to show the molecule in two representations, for instance surface and sticks (the sticks being hidden under the surface), and have the surface fade away so that the sticks become visible. Fading amount is determined by percent visibility, with the user choosing to fade from a certain percent visibility to a different percent of visibility over a specific action length. (figure)

Backbone Trace

Insertion of an alpha-carbon backbone trace of the molecule (intended for use with proteins). The trace first hides the entire protein, and then slowly builds the protein backbone by adding one residue to the trace every frame. The trace begins at a specified residue and ends at another specified residue. The user cannot specify an action length because the action length here depends on the number of residues in the trace. (figure)

Add Pause

Insertion of a pause into the movie. This is not a hard-fast pause, as actions can still be inserted into the frame range during which the pause takes place. Also, it is pointless to use this function to insert a pause in the middle of the animation, because any frame range lacking action that is bounded by two actions, is automatically a pause of action. The purpose of this button is to allow the user to insert a pause at the end of the movie. (figure)

Add Stop

Insertion of a stop command. When the movie is played, and it reaches the frame with the stop command, the movie will stop until the user presses the play button in the PyMOL GUI to resume the movie. Stops are useful for automatically stopping the movie at specific points, so that during a presentation, the presenter may have as much time as necessary to explain before continuing the movie at his or her leisure. (figure)

Make Morph *

Creates a morph between two molecules. A morph is a visual transformation of one molecule into another. Generation of the morph relies on a module in PyMOL entitled RigiMOL, which interpolates intermediate structures between the starting structure and the ending structure in the morph. Only molecules with matching, or very similar, chemical make-ups can be morphed. Morphs can be used to visualize conformation changes in proteins, or ligand docking. It is important to be aware, however, that the intermediate structures of the morph are not real, rather they are interpolated structures created to provide intermediate states between the two molecules being morphed. Note that the 'Make Morph' button only makes morphs; the morphs are included in the movie by 'Add Morph to Movie'. (figure)

Add Morph to Movie

After a morph has been created using 'Make Morph', the user can add it to the eMovie. The morph can inserted at any frame and played forward, backward, or in a loop. A loop first plays the morph in the forward direction, then pauses for a user-specified number of frames, and then plays the morph in the backward direction. (figure)

Load Previously Made Morph

Load a morph (previously made using eMovie) from a file into the movie. At this point the morph is now available for use in the movie, but must still be inserted into a specific location in the movie using 'Add Morph to eMovie'. (figure)

View Storyboard

At any time the user may click this button to view the current list of actions included in the movie, also called the storyboard. The storyboard displays each action along with the frames the action takes place in and any extra information about the action. The storyboard is invaluable during the creation of movies to check what actions have already been included in the movie, and at what frames. Actions on the storyboard may be selected and edited or deleted at any time. (figure)

Save eMovie

Saves the current eMovie to a file. The user provides a filename and two files are saved: filename.pse (a PyMOL session file), and filename.emov (an eMovie file), both necessary for later loading of the eMovie. (figure)

Load eMovie

Load a previously saved eMovie. The user provides a filename and loading takes place from two previously-saved files: filename.pse and filename.emov (eMovie automatically generates these two files when a movie is saved using eMovie). (figure)

Export eMovie

Export the eMovie as a sequence of numbered images (.png) with a specified title. For higher quality movies, the user can also choose to ray-trace each frame before its export to an image file. (figure)

(*) To make use of the morphing feature, eMovie requires a special, subscription version of PyMOL called iPyMOL (incentive PyMOL) that includes the morphing module RigiMOL. When eMovie is run on normal PyMOL rather than iPyMOL, the "Make Morph" button is hidden.

Stacking commands works. The user can specify several actions to take place on the same or overlapping frame range. Actions can also be assigned during morphs (like fading of a ligand). A stipulation, however: actions assigned during morphs should take place entirely within the frame range of a morphing action. In other words, if you have a morph in frames 50 - 80, any action applied should either span from frames 50 - 80, or be entirely contained within this frame range. This restriction stems from the fact that morphs involve changes in the states (PyMOL 'states') of the displayed molecules, while in all other parts of the movie, the states of the molecules remain constant.