Pymol background
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There are two ways to set the PyMOL background to be transparent.
1) Open PyMOL your usual way, then turn off the opaque background(default is on) by click in the menue bar on Display -> Background -> Opaque. Now you can ray trace and save your image as a png file.
2) You may add the commad set ray_opaque_background, off to your script or on the command line.
Enjoy!