Four 3D molecular visualizers compared
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  as well as a library of 3D molecular structures  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.
- 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/
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