Animations By and For the Common Researcher

Tom Goddard
February 26, 2009

We develop the UCSF Chimera visualization program which allows molecular biology researchers to create simple animations (e.g. spin or morph) to illustrate their work. Six people in our lab work directly on developing the Chimera molecular visualization software. Chimera's most distinguishing feature is its usability. This talk will consider how usable video is as a communication method for biologists for explaining results to other researchers.

Yesterday's biology research talks: 1) transfer messenger RNA clearing stalled ribosomes, 2) chaperonin open and closed states, 3) phage T4 tail contraction. Good examples of how biologists talk to biologists and benefit from animations in their explanations. The use of animations was far above typical standards -- being presented at an "animation" workshop and coming from the top labs in the world in their research areas (Joachim Frank = ribosome EM, Wah Chiu = high res cryoEM, Michael Rossman = virus EM).

Questions

• How can simple animations help communicate molecular and cellular structural biology research?
• How are animations used in journal articles today?
• What are the difficulties for a biology researcher making and publishing simple animations?

Why use video? Biological structures are three-dimensional

Prion NMR structure paper.

Figure 2E. Cross-eye stereo pair from journal article. Text describes spatial relation between residues 129 and 178 in lower right corner and their implication for a fatal familial prion disorder.

Animation. Which residue is in front D178 or M129? How far apart are they? The blue strand separates these residues as is easily seen in the animation but hard to see in the figure.

Superpositions

RNA hairpin, 20 NMR models.

Superposed models are visually more complex. Animation is especially effective in these cases using morphing -- conveying the differences in time instead of in space. Spin or morph. yMorph done in Chimera using Kreb's and Gerstein morphing algorithm using the same used by the Yale morph server.

Movies in Science Magazine February 2009 - February 2010

• 940 research articles in Science, Feb 2009 - Feb 2010.
• 91 articles include movies in supplementary material.
  • Breakdown of 91 articles with movies by subject matter:
  • 17 - molecular and cellular biology structural models
  • 27 - optical microscopy raw data (flurescent molecules in cells)
  • 25 - large animals (bats catching moths)
  • 22 - not biology (clouds on mars)
• 5% - 10% of molecular and cellular structure articles included animations.

Articles in Science Magazine with Animations

17 articles on molecular and cellular structural biology in Science Feb 2009 - Feb 2010 that include movies in supplementary material are shown below.

• 15 of 17 articles use movies that are simple enough to make in Chimera.
• Other two are an animated 2-d diagram plus graph, and cinematography of a microarray.
• In most articles the apparent effort put into making animation was low, less than effort put into a typical journal article figure.

Cryo-EM Model of the Bullet-Shaped Vesicular Stomatitis Virus (6, spin, fits)	Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1 (2, spin, morph)	Crystal Structure of the Nuclear Export Receptor CRM1 in Complex with Snurportin1 and RanGTP (1, spin)	Selective Erasure of a Fear Memory (1, spin, caspase in mouse brain)
Tuberculous Granuloma Induction via Interaction of a Bacterial Secreted Protein with Host Epithelium (3, spin, slice, data and model)	Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode (3, spin, slice, segmentation)	3D Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus (3, morph)	Activation of Rho GTPases by DOCK Exchange Factors Is Mediated by a Nucleotide Sensor (2, morph)
Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome (1, morph)	Structure of the Anaphase-Promoting Complex/Cyclosome Interacting with a Mitotic Checkpoint Complex (1, map morph)	Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth (4, molecular dynamics)	Tetrathiomolybdate Inhibits Copper Trafficking Proteins Through Metal Cluster Formation (1, spin, parts)
Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling (1, spin, MD, labels, density)	The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA (1, spin, labels, morph, parts)	Structures of the Ribosome in Intermediate States of Ratcheting (2, labels, coloring, diagram, parts)	Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch (1, diagram, simulation)
Reactome Array: Forging a Link Between Metabolome and Genome (1, cinematography)

Difficulties Creating and Showing Animations

• Problems creating animations:
  • Software is difficult to learn.
  • Software is difficult to use even when you know how.
• Problems playing animations:
  • Doesn't play in PowerPoint.
  • Standard movie formats don't play on all computers (stock Mac, Windows and Linux systems).
• Problems publishing animations:
  • Journals don't embed movies in online articles, instead bury them in supplemental material.
  • Animations don't replace figures -- it's just more work.
  • Is it still common to print articles on paper for reading offline?

Animation Software is Hard to Use

	movie record ; turn y 2 180 ; wait ; movie encode output ~/mymovie.mov

Fancier Animations are Harder to Make

• Maltotriose binding protein example Chimera movie script.
• Morphing, ligand docking, labeling, hydrogen bonds, surface pocket, aromatic residues.
• 50 lines, 20 different commands.

... (setup scene)

# Start recording
movie record

# Play movie sequence
reset wideview 50
wait 50
reset closeview 25
wait 25
2dlabel change title visibility hide frames 25
wait 25

# Play morph
coordset #2 1,
wait 25

# Show hydrogen bonds
scale 1.03 25
wait
hbond intermodel true intramodel false color pink linewidth 5
roll y 0.5 50
wait
roll y -0.5 50
wait

...

Alternative Methods of Making Chimera Animations

Making a Chimera animation script requires much more knowledge than knowing how to display the same steps through the graphical user interface.

1) Canned Movies

• Press a button on the graphical user interface to make a standard movie.
• Chimera has this for morphing between molecular models and for playing molecular dynamics trajectories.
• Next step: Should have this for other common movies: spinning models, slicing density maps.
• Limitation: Won't handle multi-part movies.

2) Time-line editor

Steve Ludtke developed EMANimator Chimera animation extension. Provides a time-line graphical editor for making movies. Next steps: Need to support more transitions. User interface needs to be more self-explanatory and more fool-proof.

3) Key-Frame Scripting

• Chimera could figure out the transitions between user-specified scenes.
• Two new capabilities would be needed:
  • name specific scenes (key-frames). Remembers colors, styles, camera settings, ...
  • interpolate between key frames
• Chimera would interpolate between key-frames in natural ways (moving models, fading colors, fading models in and out).
• Advantages:
  • Don't need knowledge of commands.
  • Allows composing alternate movies from saved key-frames.
• Disadvantages:
  • Not currently available.
  • May be difficult to implement.
  • Additional parameters are needed for some interpolations. For example, spinning 360 degrees has the same starting and ending state.

4) Screen Capture

Movie Recorder tool in Chimera can directly capture all frames and create a movie. Can directly capture hand motion and any scene changes done with the graphical user interface or with commands. Limitations: Produces jerky movies because motions done by hand are not smooth. If real-time rendering frame rate is slow, movie playback at 25 frames per second will make everything happen fast. Can't fine tune the result except by recapturing the whole sequence. One mistake ruins a whole sequence.

5) Commercial Screen Capture Software

• Commercial screen capture software can directly capture anything done in Chimera.
• Example software: ScreenFlow (Mac) or Camtasia (Windows or Mac).
• Advantages over built-in Chimera capture:
  • Playback speed matches actual speed independent of graphics rendering rate.
  • Easily add highlighting making a region bright to focus attention.
  • Easily add zooming to focus attention.
  • Easily add text labels.
  • Easily add voice over.
  • Produce output (e.g. Flash) formats that will embed in web pages.
  • Produce movie encodings that will play on Mac, Windows and Linux.
• Disadvantages:
  • Does not come with Chimera.
  • Costs from $100 - $300.
  • Same limitations as built-in Chimera screen capture.

Problems Playing Animations: PowerPoint

• In past years Chimera generated animations frequently would not play in PowerPoint.
• The animations would play in all other movie players.
• This is a PowerPoint problem that significantly impedes the wide-spread use of animations in research talks.
• Maybe this problem is fixed in newer PowerPoint versions?
• What to do:
  • Document working parameters. What combinations of PowerPoint version, video format, movie width and height, bit rate (quality setting), system graphics acceleration settings, graphics card and any other relevant parameters that produce correct playback.
  • Make this documentation easy to find.
  • Have Chimera movie encoding offer a "PowerPoint compatible" option.
• Limitations:
  • The capriciousness of PowerPoint may be impossible to characterize. There are companies (e.g. PlaysForCertain) that do nothing except make your movies play in PowerPoint.

Problems Playing Animations on Mac, Windows, Linux

• Are there video formats that will play on the major operating systems (Mac, Windows, Linux) without requiring special software?
• I gave up surveying movies in Nature after the some movies would not play on Mac OS 10.6 with extra codecs provided by Perian.
• Do Quicktime movies play on a stock Windows 7 system?
• How will a biology researcher embed videos on their lab web site to be played in a web browser on Mac, Windows, Linux?
• Movies embedded in this talk web page will display correctly on Mac but not on stock Windows or Linux systems. Uses QuickTime html embed.

Problems Publishing Animations with Journal Articles

Issues that publishers of journals face to embed movies in the main body of article text (so the movies can be played while text is shown).

• What cross-platform (Windows, Mac, Linux) embedded movie player to use. Other web sites (YouTube, et al) have solutions.
• Can movies be embedded in PDF format articles?
• Current movies in supplementary material are of such poor quality does it currently justify the expense of developing infrastructure to embed movies in articles?

Do some journals already provide embedded movies in article text?