09 4 / 2012
Finding a libre 2D molecule editor
So I’ve been having fun trying to find a usable libre 2D molecule editor. I’m just trying to make diagrams of some simple pyridine-based molecules, nothing fancy.
Avogadro seems a bit buggy. Odd graphics glitches (atom labels showing up as white squares, ball rendering very wrong), poor interface (no menus?). It also seems overly 3D oriented for my needs. I couldn’t find a display setting that was just black lines and letters on white.
It took me a while to get BKChem up and running. It’s written in Python and uses Tk for its GUI, but the default Macports install of Python 2.6.7 doesn’t include Tkinter. After installing Tk, I tried rebuilding Python to no avail. However, installing the port py26-tkinter did the trick.
Unfortunately, BKChem seems slow and unintuitive. Naturally I didn’t read the manual but I couldn’t figure out how to do anything (zoom, edit molecules, you name it). I suppose I shouldn’t have expected snappy responses from an interpreted language running in a cross-platform GUI setup.
