Directory of Visualization Resources

Home > Science > Chemistry > Software > Structural > Visualization

Programmes to view or analyze properties of small molecules or proteins. Some sites offer physical models.

Resources in This Category

• Avogadro

  http://avogadro.cc/
  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.

• CueMol

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

• 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.

• 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.

• 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.

• Jmol

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

• Labquip

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

• 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.

• 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.

• 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.

• PyMOL

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

• PyMolWiki

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

• RasMol

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

• 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).

• 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.

• 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.

• 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.

Related Categories

• Home > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Proteins and Enzymes > Structure

 

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