Focused as it was on biomolecular structures, RasMol represented a major advance in the area of biochemistry and molecular biology. This program, probably more than any other, brought the world of crystal structure into the hands of educators. The Jmol applet represents the third stage of an evolutionary process that started with the development of RasMol (Sayle & Milner-White, 1995 ) in 1989. We have just recently begun to learn how it can be used to enhance student understanding of the principles of crystallography and appreciation of the beauty of symmetry. The Jmol molecular visualization applet ( Jmol, 2010 ) is leading the way in this shift.
#CHANGE COLORS OF DNA IN JMOL PDB SOFTWARE#
The shift is away from licensed profit-driven software with periodic updates to openly available software with rapid community-based `immediate' development goals. The paradigm shift of the 21st century is away from monolithic programs that are designed to do a specific task on a specific platform in a specific subdiscipline of science and toward tools that are more modular, flexible and useful in a broad interdisciplinary context.
These programs – web-based, open-source and platform-independent – combine features of rapid development, expert communities and widely accessible databases with the power of the web to communicate features of molecular and crystallographic structure in creative and artistic ways that could not have been imagined in 1965. This paper focuses on a new paradigm of computer program that aims to revolutionize the area of visualization in chemical education again, particularly in the area of crystallography. In addition, specialized software and web-based tutorials specifically targeting fundamental concepts of crystallography and molecular symmetry are now available (Cass & Rzepa, 2005 Harwood & Korkmaz, 2005 Johnston, 2005, 2008 Charistos et al., 2005 Kastner et al., 2000 ). While developed primarily for research purposes, these programs have found utility in the area of education as well, as noted in recent symposia at national American Chemical Society meetings (Kantardjieff, 2005 Battle et al., 2009 ). Since then, personal computing power has increased immensely, and a number of computer programs have been introduced that allow real-time interactive construction of crystals ( CrystalMaker, 2009 Shape, 2009 ) and exploration of molecular structure and bonding in the context of databases. The introduction of ORTEP (Johnson, 1965 ) over 40 years ago made possible for the first time a ready two-dimensional projection of the three-dimensional atomic world of crystals and ushered in a revolution in molecular visualization. It goes without saying that visualization is important in the area of crystallography. Introduction – crystallographic visualization
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