Using Raster3D for Animation


The basic idea here is to repeatedly render a scene with small shifts in the contents between renderings. Here is an example of animating a 360 degree rotation of a scene described by Molscript and rendered in Raster3D.

  1. Create a Molscript description file for your scene, and make sure it works. Run it through Molscript once and note down the "window" and "slab" parameters reported to the terminal output. Add these to the top of your Molscript file so that they will be the same for all the rendered images. Also add a single line "@frame_rotation.mol" at the end of the coordinate transformation section of the Molscript input, as in the following example:
        ! File  "animate.mol"
        ! MOLSCRIPT V1.4 description file for an animation
            window 100. ;
            slab   100. ;
        ! Read in protein coordinates, center and rotate to desired viewpoint
        read PROTEIN   "protein.pdb";
        transform atom *
    	by centre position atom *
     	by rotation z    5.0
    	by rotation x   33.0
        ! Secondary structure 
            set planecolour  hsb 0.52 0.8 1.0 ;
            set plane2colour hsb 0.52 0.9 0.6 ;
            set linecolour   hsb 0.52 1.0 0.9 ;
    	strand from A4   to A9   ;	turn from A9   to A13  ;
    	helix  from A13  to A19  ;	coil from A19  to A41  ;
        [and so on and so forth]

  2. Remember to create a file "header.r3d" that contains the header records passed by Molscript to the Raster3D rendering program. Molscript will use its own header records by default if this file does not exist, but the defaults are not appropriate for your animated image.

    Your picture may look very beautiful when it fills the whole screen, but remember that most people looking at your animation will be using a machine+viewer combination that is very slow. It is best not to make your animated image large than, say, 256x256 pixels. Size is somewhat less of a problem for MPEG animations than for animated GIF images.

  3. Now you want to run this input file through both Molscript and Raster3D repeatedly, with a different rotation in the file rotation.mol each time. Here is a perl script that does a complete 360 degree rotation in increments of 3 degrees.
    	open (STDERR, ">animate.log");
        Frame: for ($i = 0.0; $i < 360.0; $i += 3.0)
    	open(ROTATION, "> frame_rotation.mol");
    	printf ROTATION "by rotation y %6.1f \n", $i;
    	$outfile = sprintf( "frame_%3.3d.jpeg", $i ) ;
    	$molscript = '/usr/local/bin/molscript -r' ;
    	$render = '/usr/local/bin/render -jpeg' ;
    	$command = "$molscript < animate.mol | $render > $outfile" ;
    	system '/bin/echo', $command ;
    	system "/bin/csh", "-c", "$command" ;

  4. You now should have a series of rendered frames called frame_000.jpeg, frame_003.jpeg, etc, where the rotation angle is coded into the file name.

  5. You can convert the entire series of frames into an animated GIF file using the ImageMagick convert command:
         convert -delay 15 -loop 0 frame_*.jpeg movie.gif
    The -delay parameter sets a minimum display time per frame in 0.01 seconds. The -loop 0 sets a flag requesting a display program to loop over the frames repeatedly.

  6. Alternatively, you can convert the series of frames into an MPEG animation. This process is rather arcane (and I certainly don't understand it very well), but the command will look something like this:
         mpeg_encode mpeg_encoding.dat
    The mpeg_encode program is available from the Berkeley Multimedia Research Center. The entire process, including input file names, encoding parameters, output file name, etc, etc, is all specified in the *.dat file. Here is one that worked for me, but I don't guarantee that the parameters are at all optimal!
        # file "mpeg_encoding.dat"
          INPUT_DIR .
          frame_*.jpeg [000-360+3]
          OUTPUT movie.mpeg
          INPUT_CONVERT    *
          PATTERN          IBPBB
          SLICES_PER_FRAME 1
          GOP_SIZE 10
          PIXEL    HALF
          RANGE    2
          IQSCALE  5
          PQSCALE  10
          BQSCALE  15
          BSEARCH_ALG     CROSS2

  7. Depending on which method of animation you chose, the command to play back your new movie is either
     animate movie.gif 
     mpeg_play -quiet -dither color movie.mpeg 
    Netscape is capable of displaying animated GIF files also, but the performance is much slower than the ImageMagick animate command. (Actually the animate command also is slow during the first couple of loops through the movie, but once all the frames are in local cache memory it whips right along. Netscape rereads the file each time, so it never speeds up due to repetition). You can configure Netscape to trigger mpeg_play as a helper application.

  8. That's it!

Bells & Whistles

The example above is specific to the use of Molscript, but the same basic idea could be used to animate a figure composed using other tools. In this case you would probably want to write a perl script that, instead of simply writing a single line for Molscript, writes out the full set of Raster3D header records. That would allow a zoom effect through changing the scale parameter in TMAT(4,4), general rotation and translation by changing the full TMAT orientation matrix, and many other special effects.

This approach works nicely with file indirection in the render input file. One could, for example, fade a surface in or out by gradually changing its degree of transparency. To do this you would describe the surface in the main input file as

    9 End transparent
And successive iterations of the animation script would overwrite the degree of transparency sepecified in "transparent.r3d" in much the same way that the rotation angle was changed in the example listed above.

Before getting too fancy you might want to look into molecular graphics packages specifically designed for animation, for example the GRAMPS language by TJ O'Donnell and AJ Olson (1981) [Computer Graphics 15:133-142]. The perl+Raster3D combination is probably sufficient for animations simple enough to view via the web, however.

- Ethan A Merritt, Sept 1997

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