Recently, among articles “in press” from Current Opinion in Structural Biology I found a paper by Thomas Goddard and Thomas Ferrin about software for visualization of large molecular assemblies. Even if the focus of this paper is not preparation of publication quality pictures, software cited there sounds familiar: Chimera, Pymol, VMD, Qutemol. The authors mention also VISION, which is a visual programming environment capable of presenting molecular data. Molecular Graphics Lab of Scripps Research Institute that works on the VISION has some other interesting tools, including PMV – Python Molecular Viewer, which I hope to cover some other time.

Anyway, this paper actually reminded me of something. I did mention that new version of Chimera can produce input for Povray, but I did not realize that it’s not the only change in this version. After upgrading to the current version I found out that it has also several “presets” of settings suitable for on-screen viewing or producing the figure. That makes preparation of the figure much faster and if you still don’t like the results you get good starting points for some tweaking.