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Science > Chemistry > Software > Structural > Visualization

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Avogadro - http://avogadro.openmolecules.net/
Open source advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers flexible rendering and a powerful plugin architecture.

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.

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.

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.

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.

http://cuemol.sourceforge.jp/en/ - http://cuemol.sourceforge.jp/en/
Free molecular structure visualization and rendering program for Windows.

http://honiglab.cpmc.columbia.edu/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.

http://jmol.sourceforge.net/ - http://jmol.sourceforge.net/
Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.

http://pymol.sourceforge.net/ - http://pymol.sourceforge.net/
A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences.

http://viewmol.sourceforge.net/ - 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.

http://www.chemicalgraphics.com/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.

http://www.cmbi.ru.nl/~schaft/molden/molden.html - 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.

http://www.ks.uiuc.edu/Research/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.

http://www.labquip.clara.net/index.html - http://www.labquip.clara.net/index.html
Plastic molecular models for constructing polypeptides and DNA molecules.

http://www.polyhedron.co.uk/dtmm/dtmm.html - http://www.polyhedron.co.uk/dtmm/dtmm.html
Desktop Molecular Modeller: A simple program for constructing and viewing small molecules and proteins in 3D with some energy calculation/minimization capabilities. Run on any PC with Windows 9X/NT. Commercial software.

http://www.teoroo.mkem.uu.se/daniels/ymol.html - 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.

http://www.umass.edu/microbio/rasmol/ - http://www.umass.edu/microbio/rasmol/
Molecular visualization freeware for proteins, DNA, and macromolecules. Freely available for Windows, Macintosh, and UNIX.

http://www1.bbiq.jp/zzzfelis/Facio.html - 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.

Jamberoo: Cross Platform Molecular Editor - http://sf.anu.edu.au/%7evvv900/cct/appl/jmoleditor/index.html
Free cross-platform application for displaying, analyzing, editing, converting and animating molecular systems.

Molcular Model Kits - http://www.hgs-model.com/
Plastic molecular structure models for research and education in science, intended especially for biochemistry.

Molegro Molecular Viewer - http://www.molegro.com/mmv-product.php
A free cross-platform application for visualization and analysis of molecules and molecular docking results.

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.

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.

OpenRasMol - http://www.openrasmol.org/
Provided for the convenience of users and software developers of open source versions of RasMol.

OpenScience - http://www.openscience.org/links.php?section=56
A directory of links to free molecule viewers and editors.

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.

ProteinScope - http://www.proteinscope.com
ProteinScope is a free program to view and create animations of Protein Data Bank PDB files.

PyMolWiki - http://www.pymolwiki.org/
User-contributed wiki to supplement the PyMOL documentation.

Review of Molecular Modelling Programs - http://www.marcsaric.de/
Reviews, screenshots, and table of features comparing over a dozen freely available molecular modelling and viewing programs.

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.

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).

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.

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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