Since converting to linux (Ubuntu 9.04) at school, I have slowly been reconfiguring my chemical toolbox. I am using SciFinder Scholar (site licence from the university) through WINE and BKChem and xdrawchem for 2D structure creation. I still need a 3D molecular viewer and builder that would replace gaussview for windows. This has been a bit troublsome so far. The first challenge is simply to "test-drive" different programs available. After reading about some of the features of a few possible programs, I settled on taking a ride in MacMolPlt 7.1. However, just to get in the driver seat, I found myself sucked down a "rabbit hole" of dependencies. MacMolPlt relies on wxWidgets which depends on the GTK+ 2.0 development package which in turn depends on several libraries: ATK, TIFF, glib, pango, and cairo...all of which I apparently did not have installed. But like Alice, I was too enticed by the prospect before me and down I went.
Building from source so far seems a bit like making a birthday cake. Since I lack the skills of both a computer scientist and a master chef, in both cases I am having to make due with getting my ingredients "from a box." What Betty has done for millions of domestics, the Synaptic package manager does for me. Most times I try to follow the INSTALL instructions and read the README and usually my configure step will fail. I found all the libraries that I couldn't build from scratch using Synaptic and once installed, my configure step for wxWidgets passed. Still this took a couple hours with lots of trial and error. I later found wxWidgets for GTK in Synaptic also.
In the end, I fulfilled all the dependencies for MacMolPlt but still got a strange error in the 'make' step.
The real surprise came when I went back to work and as applications were being reloaded, all the text displayed in GNOME was turning to empty boxes!! After panicking a little, I tried to use the 'recovery' boot option and that didn't help. After rebooting I decided to try to use my web-browser alone to back-up my files. Fortunately I have GoDaddy server space and I was able to upload my Dissertation folder. I couldn't back it up any other way as even the terminal window was broken. I had older backups on a thumb drive and my other partition, but I would have lost a little more than a day of work....too much. When I reinstalled Ubuntu 9.04 (now more experienced) I made unique partitions for /root, /usr, /opt, and /home so I won't have to worry about losing my files or programs if I "break" my installation. I am now reinstalling all my software: Opera, BKChem, xdrawchem, Tinker, JabRef, WINE, SciFinder, Filezilla, etc and downloading my Dissertation folder from my server. Only lost about 3 hours....
As always, lessons learned.
