There is a bug in a third party library that causes PyMOL to hang when reading from a pipe, if auto_defer_atom_count is set to anything but 0. If you are piping data into PyMOL, please ensure you have “set auto_defer_atom_count, 0” in your ~/.pymolrc file. We have set this value to zero by default, so most people will not be affected.

Problem: PyMOL refuses to start.

Solution: For some unknown reason, Windows Vista with SP2 causes an installation aberrance where the PYMOL_PATH is incorrectly set in the Windows registry. To verify that this is the problem, please run “regedit” and find “PYMOL_PATH”. If it is “C:\Program Files\PyMOL\\PyMOL” then please change the entry to “C:\Program Files\PyMOL\PyMOL” (remove the double slash).

PyMOL v1.4+ does not run on SLED 10.2 in 64-bit mode, due to a problem with Python 2.7 and Tcl/Tk.