I'm putting this here so that a) I've got it documented somewhere what I did to work around this, and b) so that if some other person's searching for this answer hopefully Google turns it up for them.
In pymol, in order to emulate the middle and right mouse button I needed to go into the X11 preferences and turn on the input preference to "Emulate three button mouse" and then stop and restart X11. Now, if I load a PDB into pymol I can hold down the option key and then select the structure and drag it around the canvas.
While I was at it, I also changed two other preferences:
In pymol, in order to emulate the middle and right mouse button I needed to go into the X11 preferences and turn on the input preference to "Emulate three button mouse" and then stop and restart X11. Now, if I load a PDB into pymol I can hold down the option key and then select the structure and drag it around the canvas.
While I was at it, I also changed two other preferences:
defaults write org.x.X11 wm_ffm -bool trueThe full writeup was at UCSF Computer Graphics (using some software called Chimera). Disabling these values means that you don't need to first click to select an X11 window before making it active (the old "focus follows mouse" option), and also doesn't require a click to make the window active before letting you bring up a drop-down menu.
defaults write org.x.X11 wm_click_through -bool true
