Animation

The Animation tool allows saving and restoring scenes in Chimera, placing scenes along a timeline, and recording a movie of the resulting animation. See also: Movie Recorder, Demos, Rapid Access, Chimera sessions, making movies

** Not all aspects of Chimera are included in scenes and/or handled correctly in Animation transitions (see limitations). **

There are several ways to start Animation, a tool in the Utilities category. Clicking Preferences opens the Animation preferences. Close dismisses the Animation dialog, and Help opens this manual page in a browser window.

A Chimera scene includes:

• locations and orientations of models and clipping planes (etc., as in a saved position)
• display styles, colors, and visibilities of molecule models, molecular surfaces, and their parts
• volume displays
• axis, plane, and centroid representations
• 3D labels, 2D labels, color keys
• CASTp pocket display
• certain global parameters such as background, lighting, and effects

Scenes do not include all aspects of Chimera. Scenes increase session file size.

Clicking the plus icon in the Scenes section of the the Animation dialog saves the current state of Chimera as a scene and generates a thumbnail image to represent it. Clicking the thumbnail restores the corresponding scene. Scenes can also be saved and restored with the scene command, or restored from Rapid Access.

Right-clicking a scene thumbnail raises a context menu with the options:

• Add to timeline - append the scene to the timeline
• Properties - open a dialog for editing the scene name and description
• Update - overwrite the scene with the current state of Chimera
• Delete - delete the scene^*

Clicking a scene thumbnail not only restores the scene in Chimera but also chooses the scene (highlights the thumbnail) in the dialog. Multiple scenes in a contiguous block can be chosen by clicking the first (or last) thumbnail in the block and then Shift-clicking on the last (or first) thumbnail. Ctrl-click toggles the state of a single scene. The chosen scene(s) can be collectively:

• deleted^* by clicking the minus icon in the Scenes section of the dialog
• appended to the timeline by clicking the plus icon in the Timeline section of the dialog

A keyframe is simply a scene in the context of a timeline. Each keyframe is associated with a preceding transition of one or more display frames. The timeline may also contain actions, or operations in Chimera other than transitions between keyframes.

Available Actions:

• Rock - oscillating rotation
• Roll - continuous rotation

In Animation, a scene or an action can be inserted into the Timeline by drag-and-drop, or a scene can be appended with Add to timeline in its right-click menu. One or more chosen scenes (or similarly, an action chosen by clicking its thumbnail) can be appended to the timeline by clicking the plus icon above the timeline.

Keyframes and actions can be repositioned along the timeline by:

• dragging, where Shift-dragging also moves any subsequent (rightward) keyframes and actions in parallel
• editing duration, which will also move any subsequent (rightward) keyframes and actions in parallel

The timeline contents can be played back to preview the movie that would result from recording.

Right-clicking a keyframe or action thumbnail raises a context menu with the options:

• Properties - edit properties of the action, or for a keyframe, the preceding transition
• Delete - remove the keyframe or action from the timeline

• Duration
  • Duration in frames - number of frames; if changed, all subsequent (rightward) keyframes and actions will shift accordingly
  • Nth frame for discrete transitions - frame at which discontinuous changes should occur

    Properties that change continuously include: model orientations and scale; clipping plane positions; colors and display states (faded in/out with transparency) of atoms, ribbons, and molecular surfaces; colors, display states, and positions of 2D labels. Discontinuous changes include those in atom/bond styles and volume displays. Transitions between different frames of a trajectory will linearly interpolate the trajectory frame number but use only integer values, thus duplicating or skipping trajectory frames as needed to produce the specified duration.

• Parameters - action-specific settings
  • for Rock:
    • Angle to rock through (default 60°)
    • Axis of rotation (x/y/z)
    • Times to rock (default 1)
  • for Roll:
    • Degrees to rotate (default 360°)
    • Axis of rotation (x/y/z)
    • Precess around axis (true/false) - whether to also rotate around a moving axis that is carried along by the main rotation (see the Wobble motion movie in the Chimera Animation Gallery)
    • Precession tilt (default 10°) - the angle between the moving axis and the main axis of rotation

Clicking a thumbnail in the timeline chooses the keyframe or action (highlights the thumbnail). Multiple keyframes/actions in a contiguous block can be chosen by clicking the first (or last) thumbnail in the block and then Shift-clicking on the last (or first) thumbnail. Ctrl-click toggles the state of a single keyframe or action. The chosen keyframes/actions can be collectively:

• removed from the timeline by clicking the minus icon in the Timeline section of the dialog
• dragged in parallel along the timeline

• expanded by clicking the zoom-in icon
• subsequently restored to the original size by clicking the zoom-out icon

In Animation, a red vertical line (the scrubber) indicates playback position on the timeline. Double-clicking a keyframe thumbnail moves the scrubber to that keyframe and restores the corresponding scene in Chimera. Other playback features are provided by clickable icons:

icon	meaning
	play animation; switches to a pause icon during playback, and if playback is paused, to a resume-play icon
	advance playback by a single display frame
	toggle looping during playback (brighter icon when on)

During playback, the target display rate is set to 25 frames per second, to match as closely as possible the speed of the movie that would result from recording with default encoding options (details...).

Clicking the recording icon in the Animation dialog opens a dialog with movie settings. After the necessary inputs have been specified, clicking Record initiates playing and recording the animation (as defined in the timeline) from start to finish. Recording in progress is indicated by a brighter icon, which can be clicked to abort the process; otherwise, the resulting series of images will be encoded into a movie file. Settings:

• File name - name for the resulting movie file
• File type (movie format) choices:
  • H.264 [.mp4]
  • VP8/WebM [.webm]
  • Theora [.ogv]
  • Quicktime [.mov]
  • AVI MSMPEG-4v2 [.avi]
  • MPEG-4 [.mp4]
  • MPEG-2 [.mpg]
  • MPEG-1 [.mpg]
  • WMV2 [.wmv]
  • APNG [.png] - animated PNG (lossless, settings for quality and bitrate do not apply)
• Rendering:
  • Chimera (default) - Chimera rendering, normally offscreen (details...). Images can be supersampled, that is, initially generated at a higher resolution and then sampled down to the final size.
    • Supersample (1x1/2x2/3x3/4x4) - how many pixels to sample in the X and Y dimensions for each pixel in the final saved image; thus, 1x1 corresponds to no supersampling. Higher values increase the smoothness of edges in saved images and increase calculation time with little effect on file size. 3x3 is generally recommended when supersampling is done.
  • POV-Ray - raytrace with POV-Ray. This rendering option is the slowest but includes fancier effects such as high-quality shadows. The POV-Ray Options button opens the corresponding preferences.

• Quality (highest/higher/high/good/medium/fair/low) - higher quality corresponds to higher (variable) playback bit rates and a larger movie file, assuming the same window size and movie frame rate
• Image format - image file format (however, PNG will be used regardless of this setting if raytracing is done):
  • JPEG [.jpeg]
  • PNG [.jpeg]
  • PPM [.jpeg] (default)
• Additional recording options - options are the same as for the command movie record; if this field is left blank, image frames will be saved with default names in a default location (but normally deleted after movie encoding, depending on the encoding options)
• Additional encoding options - options are the same as for the command movie encode; if this field is left blank, the movie will be encoded to play at 25 frames per second, and image frames will be deleted after the movie has been encoded

Clicking the storyboard icon in Animation opens a dialog for specifying a directory in which to save storyboard files. The files include index.html, with HTML title as specified in the save dialog, and three files for each scene in the timeline:

• scene_name.html - WebGL export
• scene_name.png - full-sized image
• scene_name_tn.png - thumbnail image

Across the top are thumbnails of the keyframes in the order in which they appear in the timeline, with consecutive keyframes that are the same scene collapsed into a single entry. The central panel shows either the static image or the 3D-manipulable WebGL rendering of a scene. Clicking a thumbnail or navigating the series of thumbnails with the keyboard left and right arrows updates the central panel to the static image of the corresponding scene. Pressing the l (letter ell) key or clicking Load 3D Data loads the corresponding WebGL data into the central panel. When WebGL is shown, the corresponding static image can be obtained again by clicking Load Image, or by clicking in the browser window outside of the central panel and then pressing the i key.

Several problems with scenes and/or Animation have been reported, including those related to:

• gradually fading out surfaces
• trajectory playback with molecular surfaces
• molecular surface if atoms added or deleted
• hiding/showing PipesAndPlanks representations
• Color Zone
• saving symmetry copies (e.g. from sym) in a scene
• saving markers in a scene
• saving a session with a molecular surface in a scene