On Mon, Dec 19, 2011 at 10:24 AM, Francis E Reyes
I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working.
Can future builds keep the internally distributed pymol as walled in as possible?
Which installer did you use? I've found it extraordinarily difficult to keep OS X from doing various truly stupid things with the package-based installer - it took me several days just to figure out how to prevent it from overwriting Python installations elsewhere on the system. (Apple's support for their installer tools is nearly nonexistent, presumably because distributing software this way doesn't allow them to skim off a 30% cut of the sale price.) So, I'll see what I can do, but it may be a "feature" that is difficult to disable. Maybe it's time to stop distributing PyMOL with Phenix? Version 0.99 is quite obsolete at this point, and it's relatively easy to install. -Nat