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).


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.


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

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.

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

Animation Software is Hard to Use

Making a movie that spins models 360 degrees in Chimera:

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

Command scripts are used to create movies in Chimera.

  • 90% of Chimera users don't know any of these commands.
  • Average time to learn this spin movie command sequence from Chimera documentation: 1 hour (estimate).

Fancier Animations are Harder to Make

... (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
hbond intermodel true intramodel false color pink linewidth 5
roll y 0.5 50
roll y -0.5 50


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

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

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

Problems Playing Animations: PowerPoint

Problems Playing Animations on Mac, Windows, Linux

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).

Do some journals already provide embedded movies in article text?