what do you mean by it's not installed? What's your manual step?
Please use /bin/sh instead of /bin/bash in bin/pymol
fixed in rev 4188
Showing surface with the legacy APBS plugin and PyQt PyMOL interface works for me on Linux. They way how pdb2pqr is imported is messy, that could ceratinly be improved.
these plugins can be disabled in the Plugin Manager (Plugin > Plugin Manager > ... > [ ] Load on startup). After that no Tkinter errors should be raised.
It's possible to select the tk interface over pyqt at run time like this: pymol -N pmg_tk
what kind of graphics card and driver? (though I'm not familiar with the driver situation on BSD) which Qt version? (e.g. 5.6) "blinking" indicates that the context doesn't have double buffering. Try forcing mono (skipping quad buffer request) by launching with "-M": pymol -M