wiki:Animation

Version 88 (modified by Darren Weber, 15 years ago) ( diff )

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Chimera Animation Project

Preliminary Goals (not specific)

Use and program Chimera. See the ​Chimera documentation, including ​commands, ​programmer's guide, and ​example scripts. My wiki notes on additional development features for Chimera.

Notes on animation discussions for Chimera.

Notes on specific development tasks for animation.

Chimera user guide, tutorials and workshops

Chimera: current examples of movies and animation

Chimera: color and lighting background

Animation Workshop

Consider ​computer animation as an extension of computer graphics for molecular data. What are the tools and functionality most needed to produce high-quality animations of molecular structures and processes for scientists, publishers, and educators.

Animation Workshop Notes

  • Workshop discussion on animation purposes at the end of ​http://plato.cgl.ucsf.edu/Workshops/AnimationWorkshop2010/Videos/3-YZ.mov
    • Animations for communication and education (animations without physical systems restrains or models)
      • Proposed specialty in medical illustration for biochemical systems
      • Multidisciplinary teams including chemists, biologists, computer scientists, illustrators, animators, etc.
    • Animations for scientific discovery, using physical systems
      • Physical models for biological systems require super-computer simulations
      • Physical simulations at the atomic level run in time-frames with very fine temporal resolution (<= ns), which is about an order of magnitude finer than biological systems simulations (>= ms)
      • Is it premature to expect physical modeling to apply to cellular biochemical systems?
        • Rapid advances in computing systems will enable faster calculations for better functionality
          • For example, uses of graphics processors can produce 10x to 100x faster processing
        • Expensive, pre-computed trajectories can be saved and replayed in visualization software
    • Animations for insight and discovery or publications?
      • Scientists may use short real-time, interactive animations to gain insight into systems.
      • Detailed or complex animations or graphics may be time consuming, only required for important communications.
      • Course modeling and rendering for quick, easy perception vs. artistic modeling or rendering for publications.
  • Workshop discussion on animation software at the end of ​http://plato.cgl.ucsf.edu/Workshops/AnimationWorkshop2010/Videos/3-YZ.mov
    • Movie studio packages vs. molecular software packages
    • What about integrated systems for "live" molecular models in animation suites?
    • Learning animation suites (​Maya, ​Blender, etc.)
      • Graduate programs for scientists to specialize in scientific visualization.
      • Animation suites have considerable learning curves.
      • Collaborations between content scientists and visualization specialists.
    • Most scientists have not learned animation suites.
      • Most scientists do not have time to learn complex software to create sophisticated animations.
      • Scientists interested in molecular animations are familiar with chemistry packages (​Chimera, ​pymol, ​MGLTools, etc.)
      • How do we facilitate simple animations for scientists?
  • Molecular animations for education
    • ​Virtual Cell Animation Collection
      • ​YouTube Channel
      • Simplification of complex systems to focus on key concepts relevant to specific education levels
      • ​artistic license
        • Molecular model simplifications (abstractions, not atomic representations)
        • Transparency, cutting planes, etc.
        • Spatial scales and temporal scales adjusted for education
          • trade-offs between difficulty of physical simulations vs. concept clarifications
          • where technology enables physical simulations, they may be preferable
      • Annotations and audio narrations for clarification and explanation
        • Narrations start with an outline provided by content specialists (professors)
        • The outline is revised and transcribed into an audio track
        • The audio track becomes the time-line for storyboarding animation
        • Review of storyboard may generate revisions in narrative content
        • Generally storyboard is a continuous "shot", but sometimes additional "insets" may elaborate specific points
          • Care is taken not to move around into too many different "shots"
          • Consider "movie grammar" (e.g., don't cross the view axis)
        • Learning (retention) may be better with text-book reading followed by animations
      • Hands-on work with animation package (​Maya)
        • Novice undergraduate students - 1.5-2.0 months learning curve
        • Lengthy production times
          • e.g., initial creation and academic review for transcription animation was about 12 months work
          • production process can be streamlined over time
          • staff turnover incurs time for training
    • The ​Protein Data Bank
      • The PDB has ​educational resources, including a "Molecules in Motion Kiosk" for animations.
      • Automated algorithm for rotations and focus on 'special' components of PDB structures (e.g., heme in hemoglobin).
      • Available as open-source in the ​BioJava project (cf. ​BioPython, ​BioPerl).
      • PDB also interested in ​MolSoft browser.
        • Useful combination of text with hyper-links to molecular views in 3D viewer, using smooth animated transitions between views, transparent surfaces, etc.
      • PDB preference is for EASY installation (e.g., java web-start).
      • PDB requirements for animation:
        • By types of entities:
          • ligand binding and binding sites
          • conformational changes and morphing (apo/holo, active/inactive forms)
          • enzyme catalysis
          • molecular machines
          • large assemblies - atom level to maps
          • looking inside large structures
          • molecular entities in the context of organelles and cells

General Phases of Production in 3D Animation

  • Audience, Content and Goals
  • Outline and Storyboard
  • Modeling and Detailing
  • Surfacing and Lighting
  • Animation and Dynamics
  • Rendering
  • Compositing and Editing
    • Integration of narration and computer animation
    • Audio complements visual presentation (preferred to sub-titles or annotations)

MGLTools "Scenario"

Scenario’s Basic Objects:

  • Interpolator: An object that interpolates between values
  • Keyframe: A (value, time) pair
  • Interval: A pair of Keyframes and an Interpolator
  • Actions: Key frames and Intervals
  • Actors: A list of actions that modify a given attribute of a Python object
  • Director: A list of Actors
  • DejaVu-Scenario Interface
    • Actors for attributes of DejaVu objects
    • e.g. Camera.translation, Geom.material

3D Animation Packages

  • All-rounders: Blender, Maya, Cinema4D, 3DS Max, Lightwave, SoftImage XSI, Houdini, modo, EIAS, Carrara, Strata 3D, Truespace, Shade, Realsoft, ...
  • Modeling: ZBrush, mudbox, !FormZ, Rhino, Silo, SketchUp, Hexagon, PolyTrans/NuGraf, !T-Splines, ...
  • Rendering: Renderman, mental ray, fPrime, Brazil r/s, finalRender, Turtle, vray, Maxwell Render, ...
  • Animation/Effects: Motionbuilder, Realflow, Massive, SyFlex, Poser, Endorphin, ...
  • Compositing: After Effects, Shake, Nuke, Combustion, fusion, 3D Equalizer, Boujou, ...

Blender Development

Blender 2.5 is a redesign and reimplementation of Blender using python 3.1.

Molecular Dynamics Engines

Web services for molecular movies or animation

This one has lots of options. Seems like many are for a single image or jmol setup, but there is also an animation settings section at the bottom.

These two servers allow the user to create simple molecular movies. Will give some idea of common goals and user options for molecular animation.

UCLA Molecular Imaging Data Access Portal System (MIDAS)

SciPy 2010 track on bioinformatics:

Other software with movie or animation capabilities

Molecular Animation within Movie Suites

Commercial software

Historical Notes on Molecular Visualization

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