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AGM Build: A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules (for example proteins) * Chains with predetermined conformations * Charges and atom types according to selected Force Field
Jmol: Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. It includes a web browser applet that can be integrated into web pages, a standalone Java application that runs on the desktop, and a development tool kit that can be integrated into other Java applications.
Avogadro: Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.
Raster3D: Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
PyMOL: 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.
JChemPaint: A Java program for drawing of 2D chemical structures
V_Sim: V_Sim visualizes atomic structures such as crystals, grain boundaries, etc. V_Sim can use information from files in binary d3 format, in ascii, or in "xyz" format.
Ghemical: Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical can do all-atoms molecular mechanics (there is an experimental Tripos 5.2-like force field for organic molecules), and reduced protein models.
Zeobuilder: Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models.
VMD: Useful for viewing PDB files, etc. Relatively powerful configuration for graphical representation of molecule.
The CCP1GUI: The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.
OpenRasMol: RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
QMOL: Qmol is a program for viewing molecular structures and animating molecular trajectories.
gOpenMol: gOpenMol is the graphical interface into the OpenMol set of computational chemistry programs
Gdis: Gdis is a GTK based program for the display of molecules.
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.
BKchem: BKchem is free chemical drawing program with many features, written in python.
Cn3D: Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
Garlic: Garlic is a free molecular visualization program written for unix and unix clones.
VASP Data Viewer: A free, open source 3D viewer for molecular charge distributions.
EasyChem: EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2. Focus is on press-quality final drawings, drawing very easily ornaments (non-bonding electron pairs, ...) and exporting to EPS/PDF formats with LaTeX fonts (Computer Modern).
xyz2rgb: xyz2rgb makes pretty pictures and movies of molecules. It expects input in the form of an XYZ file, one of the file formats frequently used by computational chemists. As output, it produces one or more line-interlaced RGB files.
GAMGI: The General Atomistic Modelling Graphic Interface. GAMGI aims to be useful for: 1) the scientific community working in Atomistic Modelling, that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; 2) the scientific community at large, studying Chemistry, Physics, Materials Science, Geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; 3) teaching chemistry and physics in secondary schools and universities, even inviting students to install and run GAMGI at home; 4) science promotion, in schools, exhibitions and science museums.
XMakemol: XMakemol is a program written for UN*X operating systems in ANSI C using the X, Xt and Motif libraries. It can be used to view and manipulate atomic and molecular data given in xyz format.
MOLMOL: 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.
Tessel: Tessel is a 3D "compiler" to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations. Molecular models combine balls-and-sticks, arrows and coordination polyhedra representations of pure and defective crystals, finite molecules or clusters. The Madelung potential of an ionic system can be computed and depicted on an arbitrary plane or surface. The common crystallographic cell (parallepipedic), as well as the Wigner-Seitz cell or the irreducible components of the WS cell can be easily added to the plot.
KMovisto: a free molecule viewer for LINUX and other UNIX platforms
Chemtool: Chemtool is a program for drawing organic molecules easily and store them as an Postscript, X-Bitmap, LaTeX and XFig file.
BallRoom: a tool to draw large ensembles of atoms
XBS: XBS is a simple but very useful program for plotting ball-and-sticks models of molecules or crystals under the X Window system.
XDrawChem: XDrawChem is a two-dimensional molecule drawing program for Unix operating systems.
VEGa: VEGA was developed to create a bridge between most of the molecular software packages. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.
OpenChem: A python-based program for investigating nanotechnology, molecular structures, machines, and phenomena
Chemsuite Project: Chemsuite is a set of programs intended to provide to chemists an alternative to commercial chemistry office suites.
iBabel cheminformatics and molecule viewer: This is an Applescript Studio application that provides a front-end for a variety of Cheminformatics tools. To date these include file conversion (between a vast range of chemical file formats), SMARTS-based substructure searching, similarity searching, list manipulation, overlaying using OpenBabel, a 2D viewer using JChempaint, a 3D molecule viewer using Jmol, binaries for which are now included in the iBabel application. Full description as a PDF file or in CDK news.
XVibs: A utility for animating molecular vibrations.