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PyMOL downloads as a compressed file, and it leaves behind folders when you uninstall it. PyMOL is a serious scientific tool supported by a dedicated open source community. The molecular simulations are fun to play with, but they're good enough for a PBS science show.
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 interface is well laid out and fairly intuitive, considering the program's esoteric function. Using PyMOL is surprisingly easy, even if you lack knowledge of chemistry.
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It runs in Windows, Mac OS, Linux, and Unix. It will also render artistic visualizations of geometric figures, interactive visualizations, and animated displays.
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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. But more and more research-quality software is showing up at affordable prices. You'd need a research grant to afford most science-worthy tools, though, and an advanced degree to use them. The favor's since been returned: 3D graphics have revolutionized scientific visualization.
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Reference: "Prediction of Functional Tertiary Interactions and Intermolecular Interfaces From Primary Sequence Data", PS Pang, E Jankowsky, LM Wadley and AM Pyle, J of Experimental Zoology (Mol Dev Evol) (2005), 000, 1-14.ĭownload instructions: SHEVEK is available on Github.The needs of science sparked the development of the electronic computer, which led to the PC and today's multimedia-driven world. Qnifft 1.2ĭescription: SHEVEK predicts long-range tertiary interactions within RNAs, between RNA-protein and protein-protein interactions from sequence alignments. This program is available from his website. Kim Sharp has developed an updated version of Qnifft that can be compiled for both Linux and SGI platforms.
Qnifftĭescription: Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids.
An older version of AMIGOS II is available as a standalone Java applet at Github or through SBGrid. AMIGOS IIIĭescription: AMIGOS III allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures within the PyMOL molecular graphic system.ĭownload instructions: AMIGOS III is available as a PyMOL plugin at Github. Note: RCrane and Coot are also available through SBGrid.
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The source code for RCrane is available on GitHub. Coot downloads are available for Linux, Windows, and Mac. RCrane will then be accessible through the newly-created RCrane menu. Once Coot is launched, go to Extensions -> RCrane launch. Acta Cryst D68: 958-995 (2012).ĭownload instructions: RCrane is included in Coot. RCrane: Semi-automated RNA model building. Semiautomated model building for RNA crystallography using a directed rotameric approach. Double-click the downloaded file (WinCoot- version.
SORRY no up to date experimental msi installer contact me for assistance.
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Acta Cryst D (2022).ĭownload instructions: The source code and binary executable for Linux, Mac and Windows can be downloaded from Github.ĭescription: RCrane allows for semi-automated building of RNA structure within Coot.Ĭurrent version: 1.1 (released September 26, 2012) View changelog Download the installer for WinCoot-0.9.4.1.exe (or look here for more options incl. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. J Mol Biol,(2012).ĭescription: CSSR assigns RNA secondary structure to coarse-grained tertiary structure. Discrete RNA Libraries from Pseudo-Torsional Space. Srinivas Somarowthu, Michal Legiewicz, Isabel Chillón Gazquez, Marco Marcia, Fei Liu and Anna Marie Pyleĭiscrete RNA Libraries from Pseudo-Torsional Space.ĭescription: Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone. Reference: HOTAIR forms an intricate and modular secondary structure Mol Cell 2016 (62) : 111-120 HOTAIR Secondary Structure Nathan Pirakitikulr, Andrew Kohlway, Brett D. Reference: The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures
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