Visualize Molecular Structures

NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms... Platforms: Matlab

Erwin Data Structures is a library that is meant to be the ultimate data structure library for mixed usage of C and C++. Arbitrary key and value types are implemented by template files that dont use C++ templates, but are instantiated by a Perl script. This way, mixed usage in C and C++ is... Platforms: *nix

Memory Structures Library (MemSL) is a complete data structures/collection classes library with memory tracing, memory debugging, entry/exit tracing, exception handling, definable memory handlers, built-in thread support, and much more. The project supports single, double, and circular linked... Platforms: *nix

Image::MetaData::JPEG::Structures is a Perl module that describes the structure of a JPEG file; it is an appendix to the main manual page of the Image::MetaData::JPEG module, which the reader should refer to for further details and the general scope. THE STRUCTURE OF JPEG PICTURES The JPEG... Platforms: *nix

Xephyrus Data Structures Tag Library provides an easy way to create and manipulate the contents of common Java data-structures such as maps and lists. Whats New in This Release: - The library was polished up. - Several improvements were made and a few bugs were fixed. - This version is... Platforms: *nix

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows... Platforms: Windows

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows... Platforms: Windows

If you are processing unicode strings and you want to print the string but run into UnicodeEncodeError all the time, this script shows you some simple steps to visualize unicode strings. Platforms: Windows, Mac, *nix, Python, BSD Solaris

Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is more versatile than the one described by Milescu, et al. Biophys. J. 91:3135-3150 and can be used as a "blind" step detector or... Platforms: Matlab

ORMA (Oligonucleotide Retrieving for Molecular Applications) is a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate one species among homologous ones. ORMA also performs an accurate selection of high-quality... Platforms: Matlab

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt,... Platforms: Mac

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small... Platforms: Mac

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the... Platforms: Mac

MOPlot is a handy visualization application specially designed for fast molecular orbitals plotting from the outputs of the Gaussian 03/98/94, Molcas, Gamess/US quantum chemical calculation packages. This Molecular Orbital Plotting Program will prove to be easy-to-use and very efficient. MOPlot... Platforms: Windows, XP

The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader. Platforms: Windows, Mac, Linux

A Fortran 95 implementation of an algorithm for generating derivative structures of a parent lattice. The algorithm is discussed in detail in: Gus L. W. Hart and Rodney Forcade, 'A new approach to generating derivative structures,' Phys. Rev B. (20 Platforms: Mac, BSD, Linux

MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list. Platforms: Windows, Mac, Linux

MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time. Platforms: *nix

PFMD performs a Molecular Dynamics simulation of some polarizable fluids at the liquid state by means of a dissociable potential. Supported molecules are H2O (water) and MX3, where M is a metal among Al, Fe, or Ga and X is a halogen among Cl, Br, or I. Platforms: Windows, Mac, Linux

PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! Platforms: Windows, Mac, BSD, Solaris, Linux