Software Codecs

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Codecs

I've made movies with the DivX codec and those, in my experience, make the best movies. They take a while to encode, and are large, but have the best output quality.

Mplayer/Mencoder

I used mencoder to make a movie. The best encoding command line was,

mencoder -mc 0 -noskip -skiplimit 0 -ovc lavc -lavcopts \
codec=mpeg4:vhq:trell:mbd=2:vmax_b_frames=1:v4mv:vb_strategy=0:vlelim=0:vcelim=0:cmp=6:subcmp=6:precmp=6:predia=3:dia=3:vme=4:vqscale=1 \
mf://*.png -mf type=png:fps=18 -o output.avi

This gave me an 18 frame-per-second divx/mpeg4 movie with superb quality. The movie is large and is at Arrestin Vs Rhodopsin (DivX). The input are all the files ending in ".png" in the current directory; the output is output.avi, the movie. The three lines are actually on long one; concatenate them at the black slashes \.

Quicktime

Recent attention to transparencies and QuickTime show that one typically wants to set

set ray_opaque_background, off

to tell PyMol to stop using Alpha-channel for transparencies and switch to blending.

If you're having transparency problems this could be a fix.