Application Index

This section contains software for molecular visualization. Most of them are for rendering large biomolecules such as proteins and DNA/RNA from a wide variety of file formats. Some of them are capable of displaying the molecular orbitals or the electron density resulted from ab initio calculations. Some can be used with a web browser as a plug-in.

SEQMOL is an integrated sequence alignment and PDB structure analysis utility that serves as a bridge between multiple sequence alignments and PDB coordinates. It can be used to compute evolutionary attributes of multiple sequence alignments (such as sequence conservation scores, hydrophobicity conservation, physical covariation) and to map them onto PDB files. In addition, SEQMOL hosts editable sequence alignment browser and many other unique features that were designed to speed up your research and extract valuable information from sequence alignments and from PDB files.
View Application Entry for SEQMOL

Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. It is also useful for functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.
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ViewerLite is a free software for visualization of organic, inorganic structures, proteins, DNA/RNA, and crystals.
View Application Entry for ViewerLite

The Maestro graphical user interface (GUI) allows the user to create and display complex chemical structures, start and monitor a variety of calculations, and analyze structures and results of calculations. Maestro adds uniformity across many product lines of Schrodinger Inc., as well as provides exceptional ease-of-use for each of those tools. Maestro also contains many general-purpose features which make it useful as a stand-alone product or in conjunction with third party software.
View Application Entry for Maestro

INTERCHEM is a general-purpose molecular modelling program which uses the graphics facilities of Silicon Graphics workstations for display of structures, and for molecular-mechanics and quantum-chemistry calculations. It is suited to calculations on both low- and high-molecular weight systems, and has many features incorporated for treating protein and enzyme structures. It is the cornerstone software to which many of the other programs are linked. Progrems for SGI systems: INTERCHEM General purpose molecular modelling program, PRESTO Protein sequence analysis and alignment, CHEMSPREAD Statistical analysis program. Programs developed for SGI systems that will work on other UNIX systems: THREEDOM Structure alignment program, CONVERT Structure file format conversion program, AUTOBUILD Automatic generation of libraries of 3D structures, PROTEINS Program to access a local copy of the PDB and convert file formats, ICMECH A stand alone version of a simple molecular mechanics program, STRAUSS Generates 3D structures from SMILES strings (handles stereochemistry). Programs for Microsoft Windows systems: INTERCHEM-pc General purpos molecular modelling program, PRESTO-pc Protein sequence analysis and alignment.
View Application Entry for INTERCHEM modelling software

Molecular Surface Package, a set of programs by Connolly for calculating and displaying molecular surfaces.
View Application Entry for MSP

For visualisation of crystal structure for small molecules, including packing, slicing, and visualisation of intermolecular interactions.
View Application Entry for Mercury

JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use, platform neutral, molecular visualization tool, which can be used standalone or integrated into a larger program. JMV provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. JMV loads PDB files over the web from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems.
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CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. CACTVS Tools is a visualization package for chemist.
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GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
View Application Entry for GRASP (Graphical Representation and Analysis of Structural Properties)

RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. RnaViz needs a modified version of Tcl and several extensions. Binary distributions of the modified Tcl and the RnaViz package are available for Linux and MS Windows 95.
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ICMLite and ICMLitePlus are powerful tools for the following application areas: Molecular Graphics, Mathematics, Data Analysis and Visualization, Programming and Web Development, and Structure Analysis.
View Application Entry for ICMLite

Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
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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.
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FlexV is a general-purpose molecular viewer for UNIX System V workstations. It was originally developed to be the visualization front end for the protein-ligand docking program FlexX, but because it is a stand-alone tool with easy interfaces, it can be used in combination with any kind of molecular modeling software. FlexV is based directly on OpenGL (OpenGL is a registered trademark of Silicon Graphics Inc.) which enables fast rendering as well as portability. If you do not have OpenGL available on your computer, you can use the public domain clone MESA (MESA is developed by Brian Paul, see http://www.mesa3d.org for more information.) as well. The goal of FlexV is to visualize molecules in combination with any kind of additional geometric data from simple objects like lines or dots to more complicated ones like 3D splines (for ribbons) or spherical surface patches (for interaction surfaces and connolly surfaces). FlexV is not a modeling tool. You can neither manipulate molecules nor compute anything with it except measuring distances, angles, or torsion angles. To get an impression, take a look at some FlexV screenshots.
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Gdis is a GTK based program for the display of molecules. It is in development, but is nonetheless fairly functional. It has the following features: -Support for several file types (BIOSYM, XYZ, XTL, MARVIN restart, and GULP) -A simple molecular creation and manipulation tool -A dialogue for creating starting configurations for molecular dynamics simulations -Assorted tools for visualization (geometry information, region highlighting etc.) -Molecular animation of BIOSYM files (also rendered animations) Gdis also allows you to perform the following functions through other packages: -Rendering of molecules (courtesy of povray) -Energy minimization (courtesy of gulp) Gdis is released under the GPL.
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PSI88 is a molecular orbital plotting package. It consists of PSI1 which generates is a molecular orbital plotting package, PSICON which extracts contours from the 3D data and PSI2 which produces plots from the PSICON output. Molecular orbital coefficients for semi-empirical, STO-3G, 3-21++G(*) and 6-31++G(d,p) basis sets are implemented for atoms H-Ar. PSI88 does not have a graphical user interface. For interactive display and manipulation of molecular orbitals using PSI88, ChemEdit and XChemEdit can be used. ISOVIS from NCSA at the University of Illinois at Urbana-Champaign may be used for a 3D volume visualization of molecular orbitals in conjunction with PSI88.
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MindTool is a free program for viewing/drawing molecules and simple objects such as text, lines, arrows, arc, etc. in SunView or OpenWindows environment on Sun work stations.
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Marvin is a collection of Java applications, applets, and JavaBeans for - drawing and displaying chemical structures and query substructures - interconverting several molecular file formats, like MDL Molfile, SDfile, Smiles, etc. - providing core modules for developing chemical applications
View Application Entry for Marvin Applets and JavaBeans

VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. VEGA is written in high portable code (standard C language) and can be executed on a lot of hardware systems simply recompiling the source code. The program is already tested on the following operating systems: IRIX (Silicon Graphics), Windows 9x/NT PCs, Linux, NetBSD, AmigaOS, etc.
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Pov4Grasp is a modified version of POV-Ray (a.k.a povray) running on UNIX/Linux architectures. It is mostly designed to read GRASP surface files (.srf) in their native SGI format for high-quality rendering of fully-textured molecular surfaces, just as any standard POV-Ray object. Its advantages over the official version are fast data parsing and great memory saving, especially when producing pictures and CG animations of huge molecular surfaces. For comparison, a simple GRASP to POV-Ray conversion utility (grasp2pov console tool) is also provided here, now with MegaPOV support. Source code is available for both softwares.
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QTree is a program for generating CPK, Ball and Stick and worms pictures of molecules using the quad-tree algorithm. This is a relatively fast method of generating near-photographic quality images though it does not generate shadows. A sense of depth is provided by darkening atoms farther away from the viewer. QTree provides many facilities including colouring by residue type, atom type, chain, temperature factor, or residue range, rotation, background colouring, modified lighting models and slabs through the structure. An interactive help facility is provided. Output from the program is in MTV ray-tracer format which may be viewed or converted into other formats using the ImageMagick package. QTree is freely available for use by not-for-profit organisations and for commercial organisations (providing they inform the author that they are using it). It may not be distributed without the author permission, but must be obtained from the site. It is supplied as a gzipped tar file of source code.
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RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own 2D structure space. RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of L. collosoma and sequential foldings of PSTV transcripts. RNA Movies is available for download as tar.gz source distribution or as gzip binary for the following platforms:Sun (Solaris 2.5.1), ix86 (Linux 2.0 gnulibc) and SGI (Irix 6.2, o32).
View Application Entry for RNA Movies

This is a free program which make VMD more useful but is not part of the VMD distribution. Chemical2vmd lets you use the Babel interface of VMD to load various molecular coordinate files via the .mailcap interface used by web clients like Mosaic or Netscape. Also supports the chemical/x-vmd mime type. You must have perl and Babel installed on your computer.
View Application Entry for Chemical2vmd

RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own 2D structure space. RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of L. collosoma and sequential foldings of PSTV transcripts. RNA Movies is available for download as tar.gz source distribution or as gzip binary for the following platforms:Sun (Solaris 2.5.1), ix86 (Linux 2.0 gnulibc) and SGI (Irix 6.2, o32).
View Application Entry for RNA Movies

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code. 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 provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
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JMVS (Java3D Molecular Visualisation System) is a continually developing free molecular visualisation tool implemented using Java and Java3D technology. JMVS is distributed with source code under the GNU General Public License.
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ChemDraw Net Plugin 6.0 is the latest incarnation of ChemDraw Net, with one major difference - it lives within your web browser. This means that you can access the full functionality of ChemDraw Net anywhere on the Web, without having to switch to a separate application.
View Application Entry for Chemdraw net Plugin

Chimera is a new molecular graphics package developed by the UCSF Computer Graphics Laboratory as the next generation of MidasPlus. One of the primary features of Chimera is program extensibility. This emphasis is a direct result of the success of the MidasPlus delegate extension mechanism, which has shown that the ability to incorporate user-written programs greatly enhances the modeling environment. Chimera has been designed to provide advanced molecular graphics capabilities while retaining the functionality currently available in MidasPlus. The package has been completely redesigned rather than built upon MidasPlus. Instead of combining the functionality into a single program, we selected a subset to form the core of Chimera and then implemented the rest as extensions. The three major groups of core function in Chimera are the graphical display, the user interface, and the extension mechanism.Python is the "native" command language within Chimera, so the Python command line enables the user to directly access, use, and update internal data structures. Chimera runs on SGI, Compaq/DEC Alpha, Linux, and Windows platforms.
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Flex is a simple, portable molecular graphics program that interactively displays 3D ball-and-stick models on workstations running the Xwindows system. Flex can accept input read from a file or passed over a network socket connection. The latter functionality makes flex ideal for monitoring large-scale simulations as they progress. Flex provides a library of subroutines, netg, to support this function.
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Garlic is a free molecular visualization program written for unix and unix clones.
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A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated.
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Qmol is a program for viewing molecular structures and animating molecular trajectories. Originally based on the molview demo program by Mark Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol does not try to compete with programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM, but instead opts for a fast, an easy to use user interface with a simple set of features.
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Spock is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M University. Spock has been designed from the ground up to be powerful, flexible and most of all, easy to use. Many of the features of spock are designed to bring molecular modeling programs into the age of the internet. Spock has the features users have come to expect from molecular graphics software including several bond and atom rendering types, and a complete array of backbone "worm" representations. Further, spock can calculate and display molecular and accessible surfaces, and color code these surfaces by properties (such as electrostatic potential).
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Tachyon is a parallel/multiprocessor ray tracing system designed to render images at high quality, very very quickly. It is written in C, runs on almost any platform, and achieves parallelism through the use of MPI and/or threads. Tachyon is well suited for scientific visualization as it is optimized for speed with large amounts of geometry. It has most of the features one would expect out of a good ray tracer, and has been in development for several years. Tachyon has been used to render very complex scenes containing millions of objects for molecular visualization and rendering of Mars planetary radar data.
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What is PovChem? It is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds. It then exports the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!
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The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows 95/98/NT, DOS, the Macintosh, i86 Linux, SunOS, and Amiga. The source code is available for those wanting to do their own ports.
View Application Entry for POV-Ray

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are IRIX, Linux (i386 and PPC), OSF1 and SunOS. DINO is distributed in binary form only, the current DINO version is 0.8.2. Structural Biology is a multidisciplinary research area, including x-ray crystallography, structural NMR, electron microscopy, atomic-force microscopy and bioinformatics (molecular dynamics, structure predictions, surface calculations etc). The data produced by these different research areas is very diverse: atomic coordinates (models and predictions), electron density maps, surface topographs, trajectories, molecular surfaces, electrostatic potentials, sequence alignements etc... DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set. Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates and electron densities), CHARMM (coordinates and trajectories), CCP4 (electron densities), UHBD (electrostatic potentials), DELPHI/GRASP (electrostatic potentials), MSMS (surfaces), MSP (surfaces), MEAD (coordinates and electrostatic potentials) and greyscale TIFF (surface topographs). Output can be written as TIFF, PNG, PostScript, Raster3D or POV-Ray
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Biodesigner is a general purpose molecular modeling and visualization program for personal computers working under control of Windows 95, Windows 98, Windows ME, Windows NT, or Windows 2000 operating systems. The program is freely available for downloading.
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MolPOV is a graphics file converter that reads Brookhaven Protein Data Bank format files and produces a ready-to-render input file for the Persistence of Vision ray tracer. The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. A POV setup dialog can be used to edit many of the basic scene features and rendering options. In addition, the program allows launching of the POV program to view the rendering immediately. MolPOV version 2 works with Windows 95/98/NT. MolPOV 2 was written in Visual Basic 5.0 by David Richardson, Department of Chemistry, University of Florida, Gainesville, Florida 32611. Email: der@chem.ufl.edu
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PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It is fully extensible and available free to everyone via the "Python" license. Although still early in development, PyMOL can already be used to generate molecular images and movies with relative ease.
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MolView and MolView Lite are free molecular visualization programs for the Macintosh.
View Application Entry for MolView and MolView Lite

MacMolecule 2 and PCMolecule 2 are Molecular visualization programs for students of chemistry, biology, biochemistry, cell and molecular biology, and organic chemistry.
View Application Entry for MacMolecule 2 and PCMolecule 2

gOpenMol is the graphical interface into the OpenMol set of computational chemistry programs, developed by the OpenMol development group.
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NIH Image is a public domain image processing and analysis program.
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XMol allows researchers to view (on any X11 or OpenGL display server) 3D molecular models produced by other software packages, and to print the molecular displays in PostScript, MAC PICT, VRML and other formats. Molecular models can be translated and rotated in a variety of ways. Animations of multi-step datafiles are possible, as are the calculations of atom-to-atom distances, bond angles, and torsion angles. Modest editing features are also supported, allowing the user to change the type and charge of individual atoms.
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Hyperactive Molecules Using Chemical MIME (Multipurpose Internet Mail Extension) is a WWW Display of 3D Chemical Information.
View Application Entry for Hyperactive Molecules Using Chemical MIME (Multipurpose Internet Mail Extension)

ImageMagick is a free robust collection of tools and libraries to read, write, and manipulate an image in many image formats (over 68 major formats) including popular formats like TIFF, JPEG, PNG, PDF, Photo CD, and GIF. With ImageMagick you can create images dynamically, making it suitable for Web applications. You can also resize, rotate, sharpen, color reduce, or add special effects to an image and save your completed work in the same or differing image format. Image processing operations are available from the command line, as well as through C, C++, and PERL-based programming interfaces. ImageMagick is known to compile and run on virtually any Unix. system and Linux. It also runs under Windows 2000, Windows 95/98, Macintosh, VMS, and OS2.
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WinMGM is a molecular graphism program. It allow to display and manipulate one or more molecules. You can add ribbons, solvent accessible surface, hydrophobic/electrostatic/custom isopotentials etc. and use various display modes. WinMGM 2 currently runs on Linux Intel, solaris Intel, windows (95, 98, NT 4.0).
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ORTEX is a program for the study and display of molecular and crystal structures which is very easy to use. It is available for WIN95, WIN98, NT4 and WIN3.1.
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CONSCRIPT is a free program for generating electron density isosurfaces for presentation in protein crystallography. It allows protein electron density isosurfaces to be rendered in triangulated form suitable for input into the popular MOLSCRIPT and Raster3d packages. This method of display leads to more easily interpretable pictures and can dispense with the need for stereo-pair presentation.
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Ribbons is a commercial software distribution package for general molecular illustration and for error analysis in protein crystallography. It is available for Unix and Linux platforms.
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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. The program has been tested on following platforms: Alpha / OSF 4.0, SGI / Irix 6.2 6.5, IBM RS6000 / AIX, SUNOS (g77/gcc) and Intel Pentium / linux (Redhat 6.1, Mandrake 7.1)
View Application Entry for Raster3D

O is a general purpose macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules.The current version of the program is running on Silicon Graphics IRIS 4D and the Evans & Sutherland ESV workstations.
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WebMol is a program designed to display and analyze structural information contained in the Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application.
View Application Entry for WebMol

Cn3D is a free helper application for your web browser that allows you to view 3-dimensional structures from NCBI Entrez retrieval service. Cn3D runs on Windows, MacOS, and Unix. Cn3D simultaneously displays structure, sequence, and alignment.
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MOLEKEL is an interactive three-dimensional molecular graphics package that represents molecules as wire frame, stick, ball-and-stick. It can measures atom-atom distances, angels and torsion angels. It can also superimpose molecules, calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs. MOLEKEL uses texture mapping to color code any surface according to e.g. the molecular electrostatic potential. It can animate geometry optimizations, trajectory files and multiple coordinate PDB files. It can also display vibrational modes. It can be used only on Silicon Graphics Indigo Computers.
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Molden is a package for displaying Molecular Density 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. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphicsinstructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The Xwindows version of Molden is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. The program is freely available for academic users. It can be used on Unix or Windows 95/98/NT machines.
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Protein Explorer is a software for looking at macromolecular structure and its relation to function. It is a RasMol-like interface implemented in Chime, but that the Protein Explorer can offer much greater assistance and automation. Thus, the Protein Explorer can make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than RasMol, even for experts. Protein Explorer supports nearly all RasMol commands, plus additional Chime-specific commands. However, Protein Explorer version 1.71 Beta is much easier to use, and considerably more powerful than RasMol. Much exploration can be accomplished without learning any of the command language common to RasMol and Chime. The main goal is for novices to be able to concentrate on the molecular structure, not on the software required to see it. It can be used on Unix or Windows 95/98/2000/NT or Power Macintosh machines.
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MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.
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MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. It can be used on unix machines.
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Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density.
View Application Entry for Swiss-PdbViewer

Chime is a free program which can display molecular structure in three dimensions for Internet Explorer and Netscape Communicator. Its images look like Rasmol but it differs from RasMol in that Chime sits directly on a web page runs inside your browser as a plug-in whereas RasMol is a standalone program that runs outside your browser independently. Chime also differs in that it shows only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file. With knowledge of RasMol or CSML scripting, you can create interactive web pages.
View Application Entry for Chime