An open-source application for modeling, visualization, and analysis of biomolecule systems such as proteins, nuclear acids, and lipid bilayers. This application visualizes biomolecules by reading Protein Data Bank (PDB) files. It supports various options in rendering and coloring of molecules, and also can animate the result of a molecular dynamics simulation.
An open-source application for visualization of crystal structures and grid data that runs on most UNIX and UNIX-like platforms. This application can visualize calculation results from the following electronic structure packages: GAUSSIAN, CRYSTAL, Quantum Espresso (PWscf), WIEN2k, FHI98MD. Three-dimensional data such as electron densities and local potentials as well as Fermi surfaces can be visualized using this application.
An application for evaluation of thermoelectric properties and its visualization. Seebeck coefficients and Peltier coefficients can be calculated from output of the first-principles applications, OpenMX and TranSIESTA. Obtained results as well as electron density and density of states can be visualized.
A piece of software for obtaining crystal structure and visualizing three-dimensional data that runs on Windows, Linux, and Mac OS X platforms. It can handle 30 structure data formats and 17 volumetric data formats for input, and 13 structure data formats and 6 volumetric data formats for output. It is distributed free of charge in binary format for noncommercial purposes.
An open-source multi-purpose application for modeling and visualizing molecules (biomolecules, in particular). This application has been developed for multi-scale molecular simulation, and also provides a simple GUI for AMBER and Gaussian. It also implements exchange of protein residues and the Pathways model for the electron transfer in proteins. It calls rasmol for visualization of atoms and molecules.
An official Gaussian-series payware for molecular visualization. Must be used with Gaussian, the well-known software of quantum chemistry calculation. This application provides many functions such as molecular modeling, parameter setting, job management and visualization of calculation results. It also performs input file generation for Gaussian, and supports read/write of files with other formats such as Sybyl, Molden, PDB and CIF.
An open-source application for visualization of many-particle systems. With simple operation by graphical user interface (GUI) or by command line, this application can visualize particle positions obtained from molecular dynamics simulation as well as three-dimensional scalar quantities such as potential energies. It supports various display options on kinds and shapes of particles, and can also visualize bond formation between particles.
A payware for modeling and visualizing molecules. This software includes a standard editor, ChemDraw, and can perform modeling from chemical structural formula. It implements structure optimization and molecular dynamics by molecular mechanics, and provides useful GUIs for MOPAC, Jaguar, GAMESS, and Gaussian. It can also perform spectroscopy analysis. It is included in high-end packages such as ChemBioOffice and ChemOffice.
A tool of input-file preparation and visualization for xTAPP, an application of the first-principle calculation. By graphical user interface (GUI), this application helps xTAPP users for making input files, and visualizes results of wavefunctions, electron densities, and potential profiles into three-dimensional graphics from output files.