I spent the weekend updating my MacBook Pro to Mountain Lion, this took much longer than I expected due to the fact that apparently my BT business hub is prevented from downloading any files greater than 2 GB. After several discussions with the BT online help they reconfigured things to allow the 4.2GB download. It seems they have had many thousands of complaints so I added my name to the list.

The download and update went very smoothly, I then installed X11. As I mentioned previously, X11 is no longer included as part of the standard distribution of the operating system. In the future this will be downloaded when needed from the XQuartz server. This happens even if you have previously installed XQuartz.

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.

I also needed to install the latest version of Java, you will be prompted to install the first time it is required or you can use the command line. First open a Terminal window, then type

java -version

you should get a message stating “No Java runtime present, requesting install” followed by a window prompting you to install Java SE in order to open “java”, click “Install” to get the latest version.

So far I’ve done preliminary tests on the following applications without obvious issues.

Aabel Avogadro BBEdit ChemBioDraw 13 ChemDoodle DevonThink Pro Elemental MarvinSketch MarvinView MarvinSpace MOE (X11 enviroment) PYMOL Swiss-PdbViewer Vortex