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Image Viewers and Editors

Red - Costware Green- Freeware/Shareware

Site Name and Link

  Brief Summary of Site

ArgusLab Viewer for proteins, gaussian, pdb, etc. Can also do some molecule building. Pretty good tool.

Batch Man BatchMan (Batch Manager) runs under Windows (9x and NT). It is both a viewer and an interface to MOPAC and GAMESS.

Biomer Biomer is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics.

BobScript I think for printing X-ray data. You need to get MolScript (see below) first.http://www.strubi.ox.ac.uk/bobscript/

Chime Chime can be used to prepare Web based presentations and tutorials featuring "live" chemical structures.

ChemWeb ChemWeb is a chemical structure drawing program for Windows or Macintosh. The program helps you draw and save structures as GIF files making it easy to publish and distribute 2-D structure files over the World-Wide Web.

CLiDE CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of
printed chemistry literature.

DINO DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i386, OSX, IRIX, OSF1 and SunOS. DINO is distributed in binary form only, the current DINO version is 0.9.0.

Ghemical Ghemical is a computational chemistry software package released under the GNU GPL. It has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.

ExPASy
This takes you to a site where you can get the viewer SWISS-PROT, a beefed up version of Rasmol. It has a lot of other stuff too, and is worth a visit.

ICM Browser ICM Browser is a bioinformatics, computational biology and chemistry software tool called ICM Browser. Some of the highlights of this graphical user interface are a structure database (PDB) search and visualization tool, sequence analysis, color, annotate and edit sequence alignments, structure annotation, and molecular graphics and movies.

Java Molecular Viewer The Computational Center for Macromolecular Structure (CCMS) is distributing and supporting software for the determination and analysis of the structures of biological macromolecules.

JMOL Jmol is a free, open source molecule viewer (visualization and measurement). Jmol is an active project. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.

JMV JMV, a molecular viewer written using Java and Java 3D, can be used to view molecular files stored within the BioFS, BioCoRE's shared filesystem. JMV provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities.

Marvin Marvin is a collection of Java tools for drawing and displaying chemical structures, substructures and reactions. Documentation for Marvin can be obtained here.

Maestro Maestro is the unified interface for all Schrödinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers. Free to academic users.

MEAD MEAD (Macroscopic Electrostatics with Atomic Detail) is a macroscopic dielectric model of macromolecule--solvent system. The macromolecule is treated as a low
dielectric medium immersed in a high dielectric solvent, and the electric potential is determined by the Poisson--Boltzmann equation, which is solved by finite-difference methods. MEAD is free software that you are welcome to download.

Mercury Mercury offers a comprehensive range of tools for structure visualisation and the exploration of crystal packing.

MOIL-View MOIL-View is a program designed to allow the user to view and analyze molecular structures and dynamics.

Molecule Viewer Molecule Viewer (Axxiom, Lite Edition) is available as a free download. Molecule Viewer is a Windows application that works in a similar way to the Windows Picture and Fax Viewer that is part of the Microsoft Windows operating system.

MOLDEN MOLDEN is a pre- and post processing program of molecular and electronic
structure generated by programs such as from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.

MOLEKEL A molecular graphics package for visualizing molecular and electronic structure data from the output of various chemistry applications (eg Gaussian, Gamess, and others).

MolScript MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.

NIH-Image NIH Image is a public domain image processing and analysis program for the Macintosh. Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files

OpenDX If you need visualization for anything from examining simple data sets to analyzing complex, time-dependent data from disparate sources, OpenDX has what you need: features and functions that let you easily gain meaningful insight into your data.

PDB3D PDB3D is a high speed 3D molecule rendering applet which has been designed specifically for viewing Protein Data Bank (PDB) format molecular structure files within web pages.

PovChem PovChem takes chemical information (in PDB format) and makes input to a freeware package called Persistance of Vision Ray Tracer (POVRay). Written for those who don't know squat about Unix.

PyMol PyMOL is a Python-enhanced molecular graphics program for Linux, Mac and Win O/S. It excels at 3D visualization of proteins, small molecules, electron density, surfaces, and trajectories. It also includes 3D molecular editing and rendered movie generation.

Qmol Qmol is a program for viewing molecular structures and animating molecular trajectories. Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM

QuickPDB A really nifty little program for displaying PDB structures. If you like Rasmol, you'll love this one.

RasMol RasMol is free software for looking at molecular structures. It runs on Windows, Macintosh/PPC computers and Unix.

Raster3D Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

RCSB This link takes you to the Protein Database. It uses Rasmol as the online viewer. Files can, of course, be downloaded.

RPluto RPluto is an X-windows tool for visualising molecular crystal structures on UNIX (including Linux) platforms.

SnagIt SnagIt is a tool to capture objects directly from your monitor. The objects can be stills or activity like MD movies and save them as AVI video files.

VEGA VEGA: An OpenGL Molecular modelling software package to manage 3D Structures on Windows Based PCs.

ViewMol Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. It is a useful viewer for ab initio types of calculations.

Virtualdub VirtualDub is a video capture/processing utility for 32-bit Windows platforms (98/NT/2000/XP), licensed under the GNU General Public License (GPL). VirtualDub is mainly geared toward processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images. It's similar to SnagIt but not as robust, though it is free.

VMD/NAMD VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.

VMD Tricks
     Theoretische Chemie Sites where people use VMD to do cool looking stuff
     Add dipole vectors to molecules...and more (scripts for VMD)

Voxel A shareware software for Molecular Orbitals visualization, which uses a technique called "Volume Rendering" for the 3D visualization of the orbital.

VRML in Chemistry You can now visualize your own PDB files by supplying a URL define the location of your file on the net. The PDB file will be converted into VRML after clicking on Prepare Model. At the moment only the following protocols are supported: http, gopher, and news.

WebMol WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application.

XMakeMol XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

XmMol XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance.

XV xv is an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them.

YASARA YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows, that finally makes it really easy to answer your questions. With an intuitive user interface and support for affordable shutter glasses, autostereoscopic displays and data gloves, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. There is a freeware version and a for fee version

Site Name and Link	Brief Summary of Site
ArgusLab	Viewer for proteins, gaussian, pdb, etc. Can also do some molecule building. Pretty good tool.
Batch Man	BatchMan (Batch Manager) runs under Windows (9x and NT). It is both a viewer and an interface to MOPAC and GAMESS.
Biomer	Biomer is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics.
BobScript	I think for printing X-ray data. You need to get MolScript (see below) first.http://www.strubi.ox.ac.uk/bobscript/
Chime	Chime can be used to prepare Web based presentations and tutorials featuring "live" chemical structures.
ChemWeb	ChemWeb is a chemical structure drawing program for Windows or Macintosh. The program helps you draw and save structures as GIF files making it easy to publish and distribute 2-D structure files over the World-Wide Web.
CLiDE	CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature.
DINO	DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i386, OSX, IRIX, OSF1 and SunOS. DINO is distributed in binary form only, the current DINO version is 0.9.0.
Ghemical	Ghemical is a computational chemistry software package released under the GNU GPL. It has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.
ExPASy	This takes you to a site where you can get the viewer SWISS-PROT, a beefed up version of Rasmol. It has a lot of other stuff too, and is worth a visit.
ICM Browser	ICM Browser is a bioinformatics, computational biology and chemistry software tool called ICM Browser. Some of the highlights of this graphical user interface are a structure database (PDB) search and visualization tool, sequence analysis, color, annotate and edit sequence alignments, structure annotation, and molecular graphics and movies.
Java Molecular Viewer	The Computational Center for Macromolecular Structure (CCMS) is distributing and supporting software for the determination and analysis of the structures of biological macromolecules.
JMOL	Jmol is a free, open source molecule viewer (visualization and measurement). Jmol is an active project. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
JMV	JMV, a molecular viewer written using Java and Java 3D, can be used to view molecular files stored within the BioFS, BioCoRE's shared filesystem. JMV provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities.
Marvin	Marvin is a collection of Java tools for drawing and displaying chemical structures, substructures and reactions. Documentation for Marvin can be obtained here.
Maestro	Maestro is the unified interface for all Schrödinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers. Free to academic users.
MEAD	MEAD (Macroscopic Electrostatics with Atomic Detail) is a macroscopic dielectric model of macromolecule--solvent system. The macromolecule is treated as a low dielectric medium immersed in a high dielectric solvent, and the electric potential is determined by the Poisson--Boltzmann equation, which is solved by finite-difference methods. MEAD is free software that you are welcome to download.
Mercury	Mercury offers a comprehensive range of tools for structure visualisation and the exploration of crystal packing.
MOIL-View	MOIL-View is a program designed to allow the user to view and analyze molecular structures and dynamics.
Molecule Viewer	Molecule Viewer (Axxiom, Lite Edition) is available as a free download. Molecule Viewer is a Windows application that works in a similar way to the Windows Picture and Fax Viewer that is part of the Microsoft Windows operating system.
MOLDEN	MOLDEN is a pre- and post processing program of molecular and electronic structure generated by programs such as from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.
MOLEKEL	A molecular graphics package for visualizing molecular and electronic structure data from the output of various chemistry applications (eg Gaussian, Gamess, and others).
MolScript	MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
NIH-Image	NIH Image is a public domain image processing and analysis program for the Macintosh. Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files
OpenDX	If you need visualization for anything from examining simple data sets to analyzing complex, time-dependent data from disparate sources, OpenDX has what you need: features and functions that let you easily gain meaningful insight into your data.
PDB3D	PDB3D is a high speed 3D molecule rendering applet which has been designed specifically for viewing Protein Data Bank (PDB) format molecular structure files within web pages.
PovChem	PovChem takes chemical information (in PDB format) and makes input to a freeware package called Persistance of Vision Ray Tracer (POVRay). Written for those who don't know squat about Unix.
PyMol	PyMOL is a Python-enhanced molecular graphics program for Linux, Mac and Win O/S. It excels at 3D visualization of proteins, small molecules, electron density, surfaces, and trajectories. It also includes 3D molecular editing and rendered movie generation.
Qmol	Qmol is a program for viewing molecular structures and animating molecular trajectories. Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM
QuickPDB	A really nifty little program for displaying PDB structures. If you like Rasmol, you'll love this one.
RasMol	RasMol is free software for looking at molecular structures. It runs on Windows, Macintosh/PPC computers and Unix.
Raster3D	Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
RCSB	This link takes you to the Protein Database. It uses Rasmol as the online viewer. Files can, of course, be downloaded.
RPluto	RPluto is an X-windows tool for visualising molecular crystal structures on UNIX (including Linux) platforms.
SnagIt	SnagIt is a tool to capture objects directly from your monitor. The objects can be stills or activity like MD movies and save them as AVI video files.
VEGA	VEGA: An OpenGL Molecular modelling software package to manage 3D Structures on Windows Based PCs.
ViewMol	Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. It is a useful viewer for ab initio types of calculations.
Virtualdub	VirtualDub is a video capture/processing utility for 32-bit Windows platforms (98/NT/2000/XP), licensed under the GNU General Public License (GPL). VirtualDub is mainly geared toward processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images. It's similar to SnagIt but not as robust, though it is free.
VMD/NAMD	VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
VMD Tricks Theoretische Chemie	Sites where people use VMD to do cool looking stuff Add dipole vectors to molecules...and more (scripts for VMD)
Voxel	A shareware software for Molecular Orbitals visualization, which uses a technique called "Volume Rendering" for the 3D visualization of the orbital.
VRML in Chemistry	You can now visualize your own PDB files by supplying a URL define the location of your file on the net. The PDB file will be converted into VRML after clicking on Prepare Model. At the moment only the following protocols are supported: http, gopher, and news.
WebMol	WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application.
XMakeMol	XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.
XmMol	XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance.
XV	xv is an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them.
YASARA	YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows, that finally makes it really easy to answer your questions. With an intuitive user interface and support for affordable shutter glasses, autostereoscopic displays and data gloves, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. There is a freeware version and a for fee version