Bioinformatics

Tips for PyMOL from the PyMOL mailing list

Disclaimer: All the contributions displayed on this page were made by subscribers of the PyMOL mailing list at sourceforge.net and Warren L. DeLano himself. Although i have checked most of the things listed here, i cannot guarantee that everythings works well. I cannot even guarantee that i have understood everything written on this page. Please be cautious.

Available Subtopics:

• Launching PyMOL
• Displaying biochemical properties
• Coloring molecules
• Rendering molecules
• Modeling with PyMOL
• Movies
• Advanced PyMOL features
• Python scripting

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Movies with PyMOL

• Encoding video files

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Encoding video files

Assuming you have created a lot of .png files and would like to encode a .mpeg, .avi or other video format, a number of solutions are known:

• The DiVX encoder using mplayer/mencoder? There's binaries for Unix and Windows. It makes rather nice compression on a 800x600 (probably higher). It doesn't take too long to produce the nicer quailty movies, but much longer than simply

  mencoder "mf://*.png" -mf type=png:fps=18 -ovc lavc -o output.avi
  

• Another good program for converting images into movies of different formats is VideoMach : http://gromada.com/VideoMach.html
• TMPGEnc from http://www.tmpgenc.net/ is very fast, easy to use, and produces very nice ouput (MPEG-2). Unfortunately, it does not handle images larger than 720 x 576 pixels.
• The latest Adobe Premiere recipe:
  Microsoft's MPEG4 V2, 960x720 @ 30 fps, which PowerPoint automatically treats as full-screen (due it's wacky metrics).
  Using this codec, a recent 24-second movie consumed only 4.5 MB of space, but looks much better than a 640x480 Cinepak-based movie with a file size of around ~40 MB. It definitely pays to use the latest technology
• A freeware jiffy to convert png files to an animation is imgcon, which proved to be very useful:http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html

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