Changes between Version 11 and Version 12 of Animation


Ignore:
Timestamp:
Aug 13, 2010, 1:09:48 PM (16 years ago)
Author:
Darren Weber
Comment:

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  • Animation

    v11 v12  
    99
    1010Look into the EMANimator extension, including:
    11 http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html; http://blake.bcm.tmc.edu/eman/; http://blake.bcm.edu/eman2/doxygen_html/
     11 * http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html
     12 * http://blake.bcm.tmc.edu/eman/
     13 * http://blake.bcm.edu/eman2/doxygen_html/
    1214
    1315Suggestion from Tom Goddard:
    14 ''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.''
     16> 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.
    1517
    16 Need to get screencast packages for Ubuntu 10.04, see http://screencasts.ubuntu.com/Creating_Screencasts
     18May need screencast packages, for Ubuntu 10.04, see http://screencasts.ubuntu.com/Creating_Screencasts
    1719
     20
     21----
    1822
    1923=== Chimera tutorials and workshops ===
    2024
    21 http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html
    22 
    23 http://www.cgl.ucsf.edu/Outreach/Workshops/index.html
    24 
    25 http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/Agenda.html
     25 * http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html
     26 * http://www.cgl.ucsf.edu/Outreach/Workshops/index.html
     27 * http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/Agenda.html
    2628
    2729
    2830=== Chimera: current examples of movies and animation ===
    2931
    30 http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
    31 
    32 http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html
    33 
    34 http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html
     32 * http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
     33 * http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html
     34 * http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html
    3535
    3636=== Chimera: color and lighting background ===
    3737
    38 http://www.cgl.ucsf.edu/chimera/pubimages2009/
     38 * http://www.cgl.ucsf.edu/chimera/pubimages2009/
    3939
     40
     41----
    4042
    4143== Web services for molecular movies or animation ==
    4244
    43 Database of Macromolecular Movements:  http://molmovdb.org/
    44 
    45 Yale Protein Morphing Server:  http://molmovdb.org/molmovdb/help/morph.html, including examples at http://molmovdb.org/cgi-bin/movie.cgi
     45 * Database of Macromolecular Movements:  http://molmovdb.org/
     46 * Yale Protein Morphing Server:  http://molmovdb.org/molmovdb/help/morph.html, including examples at http://molmovdb.org/cgi-bin/movie.cgi
    4647
    4748These two servers allow the user to create simple molecular movies.  Will give some idea of common goals and user options for molecular animation.
    48 
    49 Movie Maker:  http://wishart.biology.ualberta.ca/moviemaker/
    50 
    51 Protein Movie Generator:  http://bioserv.rpbs.univ-paris-diderot.fr/~autin/cgi-bin/PMG
     49 * Movie Maker:  http://wishart.biology.ualberta.ca/moviemaker/
     50 * Protein Movie Generator:  http://bioserv.rpbs.univ-paris-diderot.fr/~autin/cgi-bin/PMG
    5251
    5352This 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.
     53 * Poly View 3D:  http://polyview.cchmc.org/polyview3d.html
    5454
    55 Poly View 3D:  http://polyview.cchmc.org/polyview3d.html
    56 
    57 SciPy 2010 track on bioinformatics: http://conference.scipy.org/scipy2010/schedule.html; including talk about using python to calculate protein folding on supercomputers: http://www.archive.org/details/Scipy2010-JanH.Meinke-ProteinFoldingWithPythonOnSupercomputers
     55!SciPy 2010 track on bioinformatics:
     56 * http://conference.scipy.org/scipy2010/schedule.html
     57 * http://www.archive.org/details/Scipy2010-JanH.Meinke-ProteinFoldingWithPythonOnSupercomputers
    5858
    5959== Other software with movie or animation capabilities ==
    6060
    61 Jmol:  http://jmol.sourceforge.net/
    62 
    63 pymol:  http://www.pymol.org/
    64 
    65 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,
    66 
    67 pymol tutorials on youtube: http://www.youtube.com/watch#!v=vDlyfk2zC-k&feature=related, http://www.youtube.com/watch#!v=voIxZ-qzey0
    68 
    69 Open Mol:  http://www.csc.fi/english/pages/g0penMol
    70 
    71 Bio Studio animation: http://www.youtube.com/watch#!v=Ms_ehUVvKKk&feature=related
    72 
    73 molviz.org:  http://www.umass.edu/microbio/chime/
    74 
    75 protopedia:  http://proteopedia.org/
    76 
     61 * Jmol:  http://jmol.sourceforge.net/
     62 * pymol:  http://www.pymol.org/
     63   * pymol on youtube:
     64     * http://www.youtube.com/watch?v=EhQ4q37AUgA&feature=related
     65     * http://www.youtube.com/watch#!v=Ufzx188xWd4
     66     * http://www.youtube.com/watch#!v=h-2fQCIsBnk
     67     * http://www.youtube.com/watch#!v=ARtd-UlI37w
     68   * pymol tutorials on youtube:
     69     * http://www.youtube.com/watch#!v=vDlyfk2zC-k&feature=related
     70     * http://www.youtube.com/watch#!v=voIxZ-qzey0
     71 * Open Mol:  http://www.csc.fi/english/pages/g0penMol
     72 * Bio Studio animation: http://www.youtube.com/watch#!v=Ms_ehUVvKKk&feature=related
     73 * molviz.org:  http://www.umass.edu/microbio/chime/
     74 * protopedia:  http://proteopedia.org/