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The needs of science sparked the development of the electronic computer, which led to the PC and today’s multimedia-driven world. The favor’s since been returned: 3D graphics have revolutionized scientific visualization. You’d need a research grant to afford most science-worthy tools, though, and an advanced degree to use them. But more and more research-quality software is showing up at affordable prices. Now DeLano Scientific has upped the ante by lowering the cost of quality scientific tools to the monetary equivalent of Absolute Zero: as in “free.” Its PyMOL is a free Open Source molecular viewing engine, rendering tool, and editor that can visualize 3D molecular structure down to the atomic level, including the X-ray crystallographic structure of proteins, DNA, RNA, carbohydrates, metabolites, sugars, and much more. It will also render artistic visualizations of geometric figures, interactive visualizations, and animated displays. It runs in Windows, Mac OS, Linux, and Unix.
Using PyMOL is surprisingly easy, even if you lack knowledge of chemistry. The interface is well laid out and fairly intuitive, considering the program’s esoteric function. But there’s ample help and truly extensive documentation, including source code, at the product’s Web site, where there are even links to impressive YouTube demos. The molecular simulations are fun to play with, but they’re good enough for a PBS science show. PyMOL is a serious scientific tool supported by a dedicated open source community.
PyMOL downloads as a compressed file, and it leaves behind folders when you uninstall it. It supports 64-bit editions of Windows.
WHAT’S NEW IN VERSION 1.1R1
PyMOL is a molecular viewer, render tool, 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules.
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