Dear Bernhard,

I'm certainly not one of the Pymol 3D experts, but I've done a a few 3D 
movies in Pymol for presentations with a 3D projector. It's not much 
different from creating non-3D videos, only difference is the movies 
contains the two images side-by-side. Youtube assumes 'Cross-Eye Stereo' 
by default. After uploading the video to YouTube you have to set a 
special 3D-tag to be recognized as a 3D movie (see below). This is the 
workflow how I would do it:

1) create scenes & movie in PyMOL and write out consecutive frames 
(PNGs) with 'Cross-Eye Stereo' activated

2) Merge the PNG-frames to a (video-compressed) movie using a suitable 
program of your choice (e.g. VirtualDub) employing a compression codec 
(e.g. MJPEG)
(for help on video formats supported by YouTube see: 
https://support.google.com/youtube/troubleshooter/2888402?hl=en&ref_topic=2888648)

3) Upload the Video to Youtube, add the following tag: yt3d:enable=true.
(for help on YouTube formatting tags see: 
https://support.google.com/youtube/answer/146402?hl=en&ref_topic=2888648)

I also found a tutorial which describes the process coming from a 
slightly different background than structural biology ;-) but the 
procedure is similar. Maybe this is helpful...
http://www.3dsview.com/2011/12/12/3ds-view-tutorial-how-to-convert-3ds-videos-to-youtube-3d/

Good luck!
Christoph

Bernhard Rupp schrieb:
> Dear Pymol Experts,
>
> As an activity for the International Year of Crystallography 2014 , a
> colleague of mine
> would like to produce a 3D movie that can be uploaded to the YouTube 3D
> channel from pymol
> and/or povray. We would like to know if this is (a routine action / possible
> / or a development task). If the former, where to go for instructions?
>
> Best regards, BR
>
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