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<html>
<head>
<title>Using Raster3D for animation</title>
<LINK REL=stylesheet HREF="r3d_docstyle.css" TEXT="text/css">
</head>
<body>
<h1 align=center>Using Raster3D for Animation</h1>
<h4>Example</h4>
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.
<p>
<ol>
<li> 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:
<pre>
!
! File "animate.mol"
! MOLSCRIPT V1.4 description file for an animation
!
plot
<font color=#AA0000><b>window 100. ;
slab 100. ;</b></font>
!
! 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
<font color=#AA0000><b>@frame_rotation.mol</b></font>
;
!
! 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]
</pre>
<p>
<li> Remember to create a file "header.r3d" that contains the
<a href="/man/render.html#sample_header">header records</a>
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.
<p>
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.
<p>
<li> 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.
<pre>
#!/usr/local/bin/perl
#
#
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;
close(ROTATION);
$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" ;
}
</pre>
<p>
<li> 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.
<p>
<li> You can convert the entire series of frames into an animated GIF
file using the ImageMagick convert command:
<pre>
convert -delay 15 -loop 0 frame_*.jpeg movie.gif
</pre>
The <i>-delay</i> parameter sets a minimum display time per frame in
0.01 seconds. The <i>-loop 0</i> sets a flag requesting a display
program to loop over the frames repeatedly.
<p>
<li> Alternatively, you can convert the series of frames into an MPEG
animation. This process is rather arcane (and <i>I</i> certainly
don't understand it very well), but the command will look something
like this:
<pre>
mpeg_encode mpeg_encoding.dat
</pre>
The mpeg_encode program is available from the
<a href="http://bmrc.berkeley.edu/projects/mpeg/">
Berkeley Multimedia Research Center</a>.
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!
<pre>
#
# file "mpeg_encoding.dat"
#
INPUT_DIR .
INPUT
frame_*.jpeg [000-360+3]
END_INPUT
OUTPUT movie.mpeg
BASE_FILE_FORMAT JPEG
INPUT_CONVERT *
PATTERN IBPBB
FORCE_ENCODE_LAST_FRAME
SLICES_PER_FRAME 1
GOP_SIZE 10
PIXEL HALF
RANGE 2
IQSCALE 5
PQSCALE 10
BQSCALE 15
REFERENCE_FRAME DECODED
PSEARCH_ALG LOGARITHMIC
BSEARCH_ALG CROSS2
</pre>
<p>
<li> Depending on which method of animation you chose,
the command to play back your new movie is either
<pre> animate movie.gif </pre>
or
<pre> mpeg_play -quiet -dither color movie.mpeg </pre>
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.
<p>
<li> That's it!
</ol>
<h4>Bells & Whistles</h4>
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.
<p>
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 <pre>
@transparent.r3d
@surface.r3d
9 End transparent</pre>
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.
<p>
Before getting <i>too</i> 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)
[<i>Computer Graphics</i> 15:133-142]. The perl+Raster3D combination is probably
sufficient for animations simple enough to view via the web, however.
<p>
<i> - Ethan A Merritt, Sept 1997
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