Finally I learned that in linux ffmpeg has a decent desktop capture mechanism. My initial source was from here. Much of that deals with setting up ffmpeg. The relevant piece of command to record the desktop was
/ffmpeg -vcodec mpeg4 -sameq -r 25 -vd x11:0,0 -s 1024x768 ~/screen_op.avi
This produced a video that was close enough to the original visualization. Unfortunately the video turned out to be like 300 Mb for 3 mins which was quite unacceptable.
Furthermore readablity of text was necessary. Straightforward downsizing introduced unacceptable artifacts especially to text elements.
I found Mencoder with the xvid codec to do a good job here. A small bash script to perform a 2 pass encoding:
for pass in 1 2
do
mencoder ~/screen_op.avi -ovc xvid \
-xvidencopts chroma_opt:vhq=4:bvhq=1:quant_type=mod_quant:pass=${pass}:bitrate=4000 \
-o screen_op_xvid.avi
done
Much of the docs for the options were from here and the mplayer man pages on section "xvidencopts".
In general the two pass approach with quant_type=mod_quant(2pass needed for this) seems to work well for text. I found that throttling the bitrate beyond a certain point produced unacceptable results. Further downsizing of videos upto 640x480 retained smooth animations with readable text. I managed to encode about 3 mins of video at 25 fps into about 33mb with text elements readable. I still think more can be done.
One thing that was annoying is that I could never acceptably reduce framerate from the original recording. If I did the result was either jerky or blurry both of which were not ok. As far as I understand there's no getting around unless you are willing to reduce it by an integral factor.