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Four 3D molecular visualizers compared

Conclusions

The visualization options required in modern bioinformatics have arrived on the Linux desktop. Everything you need to promote understanding of biochemical reactions is there for the taking. A huge library of molecule files in PDB format [13] as well as a library of 3D molecular structures [14] provide access to the biochemical knowledge of the world.

Besides simply representing molecules as RasMol, Jmol, and PyMOL do, Avogadro offers the ability to "design" molecules and output the resulting coordinates for calculations. The all-rounder PyMOL masters even the most complex visualizations.

As a Java applet, Jmol is excellent for developing interactive lessons and will therefore be a favorite program for biology teachers in secondary education. GChemPaint works in the opposite direction and lets you convert PDB molecular files to simple structure formulas.

Infos

Electron Density Server by the University of Uppsala: http://eds.bmc.uu.se/eds/index.html
Creating electron density maps with PyMOL: http://www.p212121.com/2009/04/16/how-to-display-electron-density-server-results-pymol/
Visualization of the DNA strand: http://biomodel.uah.es/en/model4/dna/dnapairs.htm
RasMol: http://rasmol.org
RasMol tutorials: http://www.umass.edu/microbio/rasmol/rastut.htm
Jmol: http://jmol.sourceforge.net
Teaching materials on the structure of DNA: http://biomodel.uah.es/en/model4/dna/index.htm
Avogadro: http://avogadro.openmolecules.net
PyMOL: http://www.pymol.org
PyMOL manual: http://pymol.sourceforge.net/newman/userman.pdf
GChemPaint: http://www.nongnu.org/gchempaint/
Protein Data Bank: http://www.rcsb.org/pdb/home/home.do
Protein Data Bank video tutorials: http://www.rcsb.org/pdb/static.do?p=general_information/screencasts.jsp
Library of 3D molecules: http://www.nyu.edu/pages/mathmol/library/

The Author

Karl Sarnow has been running computers since the days of the TRS-80 Model 1. As a retired teacher of mathematics, physics, and computer science, he designed early networking concepts for Linux and related applications for schools and education and has also written a book on the subject in German (http://tinyurl.com/lu1212-sarnow). Since his retirement, he has devoted his time to his hobbies: photography, traveling, and astronomy.

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