Installing pymol using macports on yosemite I tried to install pymol using macports (after trying to build from the source code failed): 

sudo port install pymol


It did install it, giving me two warnings:

Warning: xcodebuild exists but failed to execute
Warning: Xcode does not appear to be installed; most ports will likely fail to build.


I am able to run pymol, but it crashes after a minute or so. Also, the top window does not show any buttons:



The error message is:



Is this because of the warnings port gave me at the very beginning, or is there something else at work here?
In case this ever helps someone, this will make it compile and load. 

First Uninstall Pymol

Then:

% sudo port install tcl -corefoundation
% sudo port install tk -quartz
% sudo port install pymol


This is described here:

http://www.ub.edu/cbdd/?q=content/installing-pymol-macports