Progress on Chimera Animation Project

Preliminary Goals (not specific)

Learn the Chimera software package.

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

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Chimera tutorials and workshops

• ​http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html
• ​http://www.cgl.ucsf.edu/Outreach/Workshops/index.html
• ​http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/Agenda.html

Chimera: current examples of movies and animation

• ​http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
• ​http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html
• ​http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html

Chimera: color and lighting background

• ​http://www.cgl.ucsf.edu/chimera/pubimages2009/

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Web services for molecular movies or animation

• Database of Macromolecular Movements: ​http://molmovdb.org/
• Yale Protein Morphing Server: ​http://molmovdb.org/molmovdb/help/morph.html, including examples at ​http://molmovdb.org/cgi-bin/movie.cgi

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

• Movie Maker: ​http://wishart.biology.ualberta.ca/moviemaker/
• Protein Movie Generator: ​http://bioserv.rpbs.univ-paris-diderot.fr/~autin/cgi-bin/PMG

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.

• Poly View 3D: ​http://polyview.cchmc.org/polyview3d.html

SciPy 2010 track on bioinformatics:

• ​http://conference.scipy.org/scipy2010/schedule.html
• ​http://www.archive.org/details/Scipy2010-JanH.Meinke-ProteinFoldingWithPythonOnSupercomputers

Other software with movie or animation capabilities

• Jmol: ​http://jmol.sourceforge.net/
• pymol: ​http://www.pymol.org/
  • pymol on youtube:
    • ​http://www.youtube.com/watch?v=EhQ4q37AUgA&feature=related
    • ​http://www.youtube.com/watch#!v=Ufzx188xWd4
    • ​http://www.youtube.com/watch#!v=h-2fQCIsBnk
    • ​http://www.youtube.com/watch#!v=ARtd-UlI37w
  • pymol tutorials on youtube:
    • ​http://www.youtube.com/watch#!v=vDlyfk2zC-k&feature=related
    • ​http://www.youtube.com/watch#!v=voIxZ-qzey0
• Open Mol: ​http://www.csc.fi/english/pages/g0penMol
• Bio Studio animation: ​http://www.youtube.com/watch#!v=Ms_ehUVvKKk&feature=related
• molviz.org: ​http://www.umass.edu/microbio/chime/
• protopedia: ​http://proteopedia.org/