Editing Making Movies (section)

==Encoding video files==

===Animated GIF===
Quality note: Converting to video generally leads to a loss of quality and inflated file sizes. Gif animation gives a good alternative, retaining the original quality and maintaining small file sizes, however it lacks play controls. With skillful use of frame delays during the generation of the Gif it is possible to create pauses to emphasize certain frames. Ulead Gif Animator works well although there are many programs to choose from. To create files with many frames in Ulead add around 150 files as frames at a time.

===Avidemux===
[http://avidemux.sourceforge.net/ Avidemux] is a great tool to stich your image files together as a movie.  It can read the PNG output stack from Pymol and encode a movie using almost all codecs currently available. The program has an easy to use graphical interface, making the conversion simple compared to some of the other options available to you.

===Mencoder/Mplayer===
[http://www.mplayerhq.hu Mplayer] is an award-winning open source movie player.  Mencoder (which comes packaged with Mplayer) is its movie encoder.  Mencoder can take in various file formats (png,gif,jpg) and convert them to movies.

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 and 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

namely something like (this command worked BEST for my case; it's all one line connect it where the backslashes are).

 mencoder -mc 0 -noskip -skiplimit 0 -ovc lavc -lavcopts \
 vcodec=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

The mpeg4 codec requires a DivX plugin which is not a part of the default installation on some operation systems. The codec msmpeg4v2 makes movies which are more likely to be playable on standard Windows players and can be used with mencoder e.g.
 
 mencoder -mc 0 -noskip -skiplimit 0 -ovc lavc -lavcopts vcodec=msmpeg4v2:vhq "mf://*.png" -mf type=png:fps=18 -o output.avi

This encoder line is however not optimised (yet), and the codec also produces a bit larger files than the mpeg4 at the same visual quality according to the Mplayer homepage.

====Troubleshooting====
#If your movie shows up in PowerPoint with only the first frame showing, or is just a black square, try adding '''-of asf''' or '''-of avi'''.
#If the above line complains about the '''codec''' part, then replace the word '''codec''' in the command line with '''vcodec'''.

===Virtual Dub===
[http://virtualdub.sourceforge.net/ Virtual Dub] is an open-source, robust piece of software that allows easy creation of .AVI files from image sequences (such as *.PNG created by PyMol). After opening Virtual Dub, select '''File''' Menu --> '''Open Video File''' --> under "files of type" select '''image sequence (*.png, etc)'''.

After viewing (and editing) the movie, choose '''save as AVI (F7)''' from '''File''' menu.
This generates high quality, yet very large, AVI files; in order to down-size the files into formats which fit PowerPoint, free software such as [http://www.formatoz.com/download.html FormatFactory] ('''FF''') is available for download and easy use.