Update: We got positive feedback from several Yosemite users that the
latest MacPyMOL works fine for them. The X11Hybrid version works after
reinstalling XQuartz. Users have also been successfull to install
Open-Source PyMOL with homebrew.

You might also find this blog about scientific applications under
Yosemite useful:
http://www.macinchem.org/blog/files/0f5cfea643bdf4d2dfcae3991300b886-1611.php

Chees,
  Thomas

Thomas Holder wrote, On 10/18/14 08:01:
> Dear Mac Users,
> 
> if you are thinking about upgrading your Mac to OSX 10.10 Yosemite,
> please do yourself a favour and wait. We are getting a lot of trouble
> reports from users who have upgraded and now have problems with their
> PyMOL installation. In particular, the X11 Hybrid version does not
> work, neither does the free students version. We are working on it.
> Also feel free to drop me a line if you have already upgraded and
> PyMOL works fine for you or you found a workaround for any kind of
> issue.
> 
> Thanks,
>   Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

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