We too have experienced problems ourselves attempting to install X11 on Macintosh computers that have been patched since the original Mac OS X install.  The only sure fix we know of is to do a clean OS install from the original CD, being sure to select the X11 option, which is not enabled by default.  Once X11 is installed, then subsequent updates can safely be reinstalled.
Perhaps someone else on the mailing list knows of an alternate way of getting X11 onto an existing Mac?
DeLano Scientific LLC
Subscriber Support Services

From: [] On Behalf Of Frieda Reichsman
Sent: Monday, March 05, 2007 5:24 PM
To: Users List PyMOL
Subject: [PyMOL] plug-ins on Mac OSX - X11?

Dear PyMOL users,

I am a newcomer to this list and largely to PyMOL. I have a lot of experience with Jmol since my work is oriented toward publishing on the web.

I would like to be able to generate surface MEP coloring in PyMOL for proteins. I'm on Mac OSX 10.4, and I've downloaded/installed APBS and the APBS plug-in for PyMOL. Then I realized I had to install X11, so I found my original OSX 10.4 install discs, and have tried installing X11 three times with no luck (twice tried a custom install of X11 only, the third time I bit the bullet and installed the entire Xcode tools package. Still no sign of X11 on my machine.) Has anyone experienced this and found a way to deal with it?

I have already changed the name of to, as per the instructions on the web site, but when I open the newly named pymol app, it asks me where X11 is...

Thanks in advance,


Frieda Reichsman, PhD

Molecules in Motion

Interactive Molecular Structures