Chimera Animation Discussions

Translate current movie/animation examples into storyboard GUI interfaces.

• Look into the EMANimator extension, including:
  • ​http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html
  • ​http://blake.bcm.tmc.edu/eman/
  • ​http://blake.bcm.edu/eman2/doxygen_html/
• Suggestion from Tom Goddard:
  • I think that your focus now should be on learning how to make simple animations in Chimera. I think you have to be a maker of animations to productively advance the code. Being a maker of animations will give you insight into what is needed. To make your own learning about how to create animations a productive enterprise it would be great if you could make screen capture videos to explain to users how to make simple animations. Also your own making of animations could produce interesting animations that might have value on Wikipedia to elucidate biomolecules of high interest. This could link to Chimera and encourage more people to make animations. A good source of interesting molecules are the Molecule of the Month entries at the PDB. They have very nice explanations. ​http://www.rcsb.org/pdb/explore/motm.do There's not a clear sense in the community of what makes a molecular animation useful. This is a fundamental obstacle and trying to make useful animations seems like the way to attack it.
  • May need screencast packages for Ubuntu 10.04, see ​http://screencasts.ubuntu.com/Creating_Screencasts

• Chimera meeting discussion: Aug 23, 2010
  • Collaborations drive the animation gallery, they may serve a purpose to define useful animation features for Chimera, which are required by specific users who have identified limitations in Chimera.
  • Review the presentations from the ​animation workshop
  • Proposal to implement ​key frames, with a simple GUI (a storyboard with transitions).
    • thumbnail images for each key-frame (key-frames may be named)
    • 'slide-layout' GUI for arranging and navigating key-frames
    • key-frame transition GUI
      • linear interpolations (automatic for some properties)
      • motion-specific transitions
      • 'selection inspector' may provide functionality to identify and display animation properties
      • draw from the session, savepos, reset, fly etc. commands for key-frame animation classes
    • functionality to save or export key-frames
      • similar to session functionality
      • export to high-end 3D software (​Maya, ​Blender, etc.)

• Chimera meeting discussion: Oct 4, 2010
  • Reviewed initial design suggestion:
    • [[media:AnimationDesign_20101004.pdf]]
  • Short demo of pilot implementation of animation commands and GUI, e.g.:

    git clone ssh://chimera@weber.cgl.ucsf.edu/data/gitroot/chimera-extension
    # chimera-staff can obtain an ssh password for this git clone operation
    cd chimera-extension
    git tag -l
    git checkout pilot_demo_meeting20101004
    # Now startup Chimera (e.g., pre1.5-daily-build) and add extension path (Preferences > Tools etc.)
    # The demo included several commands:
    # at-chimera-command-line> open 2por
    # at-chimera-command-line> kfadd kf1
    # Manipulate model spatial properties (orientation, offset, zoom)
    # at-chimera-command-line> kfadd kf2
    # at-chimera-command-line> kflist
    # Start Animation GUI (Tools > Animation > Animation)
    # Animation-GUI buttons appear for kf1 and kf2, press buttons to call 'kfshow kf?'
    # at-chimera-command-line> kfdel kf2
    # at-chimera-command-line> kflist
    # Animation-GUI update button will display kf1 (no kf2)
    

  • Discussion notes:
    • Additional GUI for animation sequence
      • Drag-n-drop from key frame layout into an animation sequence
        • The sequence interface can be an abstract representation of a time-line, with discrete scenes and transitions between scenes
        • There can be a default transition between key frames (create a preferences setting)
        • Auto-detection of component changes between key frames
      • Features for grouping key frames into a loop sequence
      • Features for multiple instances of a key frame in the sequence
      • Options to pause a sequence (esp. at the end of a loop sequence)
      • Features to control execution of the sequence: play | pause toggle, stop, rewind, fast-forward
      • Feature to record a movie of the sequence
        • Might call up movie recorder
        • Saving animation sequence using povray rendering
    • Key frame integrity checking
      • Handle the presence or absence of model data
        • Check the existence of models and their model ID numbers
        • Are there methods to re-open a closed model (and adjust model ID numbers?)
        • Handle surface models (recreate them when opening a model or showing a key frame)
      • Delete or gray-out key frames with missing model data (e.g., a model was closed)
      • Use triggers to update GUI displays for key frames
        • Midas commands trigger GUI update
        • Triggers make GUI update button obsolete
    • Transition specifications independent of models
      • Some facets of transitions may be dependent on model components or attributes
    • Transitions for display: problems for transparency
      • Do we have or can we implement model level transparency? Is this useful?
      • Implications for core graphics engine in handing animation of transparency values
      • Currently there are problems in the display of multiple models (depth peeling issue)
      • Do we need transparency specificity for components of models (ligands, surfaces, etc.)?
    • Transition components
      • Components include: spatial, model styles, display (appearance, disappearance), color, titling (labels), clipping planes, etc.
      • Independent constructs for transitions, with potential for cumulative effects
      • Consider the EMANimator Memory GUI where states can be restored by specific components (color, motion, camera)
      • Midas command qualifications: kfshow pos <kfname> ..., kfshow camera <kfname> ..., reset color <kfname> ...
    • Animation features to include morphing (trajectories)
      • Might call up the morph utility
    • Animation sequence may be saved as a command sequence
      • Could be possible to edit the sequence code as a Midas command file or a python script
      • Could be possible to run it at a later time and edit the sequence code
      • Saving and loading a sequence command file
    • Session support
      • Key frame data structures, transitions, etc. saved to session files
    • Advanced options
      • Facility to run python code
      • A per-frame script option (as in morph utility)
    • Rename 'key frames' to 'scenes'
      • Discussion concluded that 'scene' may be a better term than 'key frame'
      • Difficulty for Midas command name with 'scene'
      • Current pilot implementation uses 'key frame' concept and term in the code
  • Animation interim milestones
    • Replace Animation GUI with Pmw scrolled canvas
    • Add key frame state properties
      • model style, color, display, etc.
    • Begin to implement transitions
      • copy and modify 'fly' or 'reset' for additional transition properties
      • explore implementing auto-detection for state changes and default transitions
      • begin with discrete transitions or linear interpolations
    • Aim to animate ligand binding
      • include on/off display transition
      • include features for loop control (including pause option)
    • Additional features dependent on completing initial milestones
      • e.g., morphing feature to come later