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PyMOL - http://pymol.sourceforge.net/
A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences. |
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VMD - http://www.ks.uiuc.edu/Research/vmd/
A free program for visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. |
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Swiss-PdbViewer - http://www.expasy.org/spdbv/
A free program for viewing and analyzing several proteins at the same time. Some energy minimzation and homology modeling features are also included. |
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Jmol - http://jmol.sourceforge.net/
Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. |
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UCSF Chimera - http://www.cgl.ucsf.edu/chimera/
Highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus. Free of charge for academic, government, non-profit, and personal use. |
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RasMol - http://www.umass.edu/microbio/rasmol/
Molecular visualization freeware for proteins, DNA, and macromolecules. Freely available for Windows, Macintosh, and UNIX. |
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PyMolWiki - http://www.pymolwiki.org/
User-contributed wiki to supplement the PyMOL documentation. |
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Grasp - http://honiglab.cpmc.columbia.edu/grasp/
A visualization and analysis program useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. Commercial software. |
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gOpenMol - http://www.csc.fi/gopenmol/
A free program for the analysis of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials. Supports many file formats like the GaussianXX, Jaguar, CHARMM, and AMBER. |
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MOLDEN - http://www.cmbi.ru.nl/~schaft/molden/molden.html
Pre- and post-processing program for molecular and electronic structure, with Z-matrix editor, electron density visualization, and molecule animations. Available for Unix and VMS; free for academic use. |
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ChemCraft - http://www.chemcraftprog.com
Windows-based program for visualization of molecular structures, vibrational modes, molecular orbitals, energy gradient and other properties from log files produced by the GAMESS and Gaussian packages. |
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Facio - http://www1.bbiq.jp/zzzfelis/Facio.html
3D-Molecular Modeling Software, available at no charge for the Windows platform. Has functions for visualization of biomolecules and results from GAMESS QM calculations, and for aligning and modifying structures. |
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PovChem - http://www.chemicalgraphics.com/PovChem/
A chemical visualization and illustration program. Reads PDB files and exports POV-Ray files for producing high-resolution ray-traced images. Available for Windows, Linux, Mac, and SGI. |
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Molcular Model Kits - http://www.hgs-model.com/
Plastic molecular structure models for research and education in science, intended especially for biochemistry. |
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Molymod Molecular Models - http://www.molecular-model.com/
Plastic molecular models for use in chemistry, biochemistry, molecular biology (DNA double helix), semiconductors and crystal lattice structures. |
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MOLMOL - http://hugin.ethz.ch/wuthrich/software/molmol/index.html
A free program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with emphasis on structures determined by NMR. Runs on UNIX and Windows NT/95. The site offers an online tutorial. |
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Nanotube Modeler - http://jcrystal.com/products/wincnt/
A program for generating and visualizing the xyz-coordinates for nanotubes, nanocones, nanosheets, and fullerenes. For Windows; free demo version available. |
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Historical Molecular Graphics - http://www.umass.edu/molvis/francoeur/movgallery/moviegallery.html
Digitized versions of 16mm movies of molecular structures produced in the early days of interactive molecular graphics. |
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Biodesigner and iMol - http://www.pirx.com/
A molecular viewer for Windows9x systems with sequence editor and protein builder. Free for academic use. Additionaly the iMol molecule viewer is available for Mac OS X systems. |
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CueMol - http://cuemol.sourceforge.jp/en/
Free molecular structure visualization and rendering program for Windows. |
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Viewmol - http://viewmol.sourceforge.net/
An open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac. Available for Linux, FreeBSD, Mac OS X, and other Unices. |
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ProteinScope - http://www.proteinscope.com
ProteinScope is a free program to view and create animations of Protein Data Bank PDB files. |
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SweetMollyGrace - http://rodomontano.altervista.org/engSweetMG.php
A suite of freeware tools for automating work of rendering and animating molecules. Generates high quality images of molecules from PDB, XYZ, or molfiles using raytracing tools (Povray and Raster3D). |
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Ymol - http://www.teoroo.mkem.uu.se/daniels/ymol.html
A free molecular visualization and animation program for the X window system. Creates images and movies, using either the built in renderer or povray. Still alpha. |
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Santorini and Patmos, Molecular Viewer and Screensaver - http://oeffner.net/development/
Read XYZ or PDB files of atoms and display them in a 3-dimensional view on Windows PCs. |
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JIMP - The Interactive Molecule Program - http://www.chem.tamu.edu/jimp/
Program for Linux and Windows for viewing and manipulating 3D structures of molecules and orbitals. Renders publication quality images and performs Fenske-Hall SCF calculations. |
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Brabosphere - http://www.brabosphere.be
Open source program for the 3D visualisation of molecular systems and their properties. It also acts as a frontend for the QM program package BRABO. Runs on various Unix platforms, Windows, and MacOS X. |
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Labquip - http://www.labquip.clara.net/index.html
Plastic molecular models for constructing polypeptides and DNA molecules. |
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Protein Explorer - http://www.umass.edu/microbio/chime/pe/protexpl/
A web-based viewer for the 3D structures of proteins, DNA and RNA. Requires Netscape and the Chime plugin, which is only available for Windows9x. |
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OpenRasMol - http://www.openrasmol.org/
Provided for the convenience of users and software developers of open source versions of RasMol. |