Crystallography on Ubuntu Linux

Ubuntu is a Debian linux distribution that is up-to-date, well-maintained, and is completely free. You just download it, burn it to a CD, and install it. It uses the Debian package management tools (dpkg, apt-get, aptitude, and so on) that has a nice front-end called synaptic. If you like using Mac OS X and the Fink package management system, Ubuntu will feel very natural.

Since you install it with a 650 MB download, not everything comes with this by default. You will have to install compilers and other dependencies in order to have everything you install work correctly. This is not a problem, as Ubuntu has a very extensive library of pre-compiled debian packages.

The only significant problem I ran into was that the Blt package that comes with Ubuntu is broken. bltwish is not to be found in any bin directory. I therefore had to rebuild it from the source code (which, fortunately, worked without a problem).

I've compiled ccp4, eden and cns "out of the box" and have installed binaries for ccp4mg, coot, phaser, phenix, usf programs, ono and pymol as well as dtrek93 and HKL2000, all of which were designed for other linux platforms (usually Red Hat). These all work without significant intervention. I haven't needed to use it, but it is worth mentioning that although Ubuntu uses the Debian package management system, there is a tool called alien that permits a user to install an rpm into Ubuntu. It does this by first converting the rpm into a deb file, and then installing it in the usual way. Ubuntu has a vast array of packages, but if you find a debian or rpm package for software that Ubuntu does not (or cannot) distribute, you can still install it with the command sudo dpkg -i foo.deb and the Ubuntu package manager will recognize the installed package. This makes systems management much less of a chore. If you want to look at the list of all the software packages that either came with Ubuntu or that I installed either on necessity or on a whim, I have that here. This is a large superset of what you would need for crystallography. I should have kept track of what was required for crystallographic programs, but I didn't.

If you install g77, g++ and gcc compilers (3.3 or 3.4), blt (from source), blas, fort77, f2c, and fftw, you should have all you need for ccp4. CNS requires bison and flex and benefits from konqueror (KDE's web browser). Eden requires fftw, gsl, grace, and python2.4, and it is good to have the numeric and scientific modules as long as you are installing python anyway. Coot has a string of dependencies, most of which, fortunately, should be present, as gnome requires many of the same dependencies. These include glib, gtk+2, glut, gtkglarea, guile, gsl, libglade2, gtk-canvas, libart2, libart2-shlibs , guile16-net-http, glut, guile16-shlibs, gsl-shlibs, libglade2-shlibs, guile-gtk, guile-www, guile-gui, guile-goosh, guile-net-http etc.

I installed all of the crystallography packages I required into a directory I created called /usr/local/xtal, permitting portability as well as helping with organization and maintenance. In the directory /usr/local/xtal/bin I have two files, one is called init.sh and the other is init.csh. By sourcing the first of these during zsh or bash startup, or the second during tcsh startup, all the environment variables and paths will be set appropriately.