Materials Visualization Tools
Molden: 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 graphics instructions; 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. Molden was also submitted to the QCPE (QCPE619), allthough the Xwindows version is considerably running behind on the current one. For more information visit: http://www.cmbi.kun.nl/~schaft/molden/molden.html.
JMol: Jmol is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. Jmol is a collaboratively developed visualization and measurement tool for scientists and educators. Some JMol features include animated results of simulations and computed vibrational modes, as well as the display of inter-atomic distances, bond angles, and dihedral angles, and vectors (velocity, dipole, etc.), charges, and atomic symbols. For more information visit: http://jmol.sourceforge.net/.
XCrysDen: XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements. The name of the program stands for Crystalline Structures and Densities and Xbecause it runs under the X-Window environment. For more information visit: http://www.xcrysden.org/.
wxDragon: The actual picture can be exported as BMP, JPEG, PNG, PNM, PCX, and TIF images (may vary on some plattforms), the geometry can be printed as an EPS-file with true scalability (no bitmap!), isosurfaces can also be printed in postscipt, the coordinates can be converted into file formats understood by related programs. For exapmple, the molecule can be exported as an input file for povray, enabling the generation of high quality pictures, and this includes the isosurfaces or other polyeder. A nice feature may be also the ability to generate povray files for the all the geometries included within the molecule (as a MD simulation or a geometry optimization), which enables the generation of a MPEG-movie. All pictures of a Simulation/geometry optimization as well as of a vibration can also be saved in various picture formats so that the generation of an animated GIF picture is quite easy. For more information visit: http://schmeling.ac.rwth-aachen.de/user/bernhard/wxd_des.html.
VMD: 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. For more information visit: http://www.ks.uiuc.edu/Research/vmd/.
Molekel: Molekel has many capabilities including an interactive, three-dimentional molecular graphics package. Melekel represents molecules as wire frame, stick, ball-and-stick and spacefill representations, and is also capable of measureing atom-atom distances, angles and torsion angles. For more information visit: http://www.cscs.ch/molekel/.
VaspView: This is a scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package , a package for performing ab-initio quantum-mechanical molecular dynamics using pseudopotentials and a plane wave basis set. The project was initiated when a chemical engineering professor requested assitance in visualizing output files produced by the above package. It displays iso-surfaces and slices of a three-dimensional data set, along with the atoms that make up the molecule the calculations were performed for, and allows symbolic bonds to be inserted between them. For more information visit: http://vaspview.sourceforge.net/.
GaussView: GaussView is capable of sketching molecules using its advanced 3D Structure Building, or load in molecules from standard files. Set up and submission of Gaussion jobs can be accomplished right from the interface, and monitored throughout the runtime. GaussView will also allow you to examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normale modes, geometry optimizations and reaction paths. For more information visit: http://www.gaussian.com/gv_plat.htm.