Graphics and Visualization

[*] AFNI (Analysis of Functional Neuroimages) is a package of computer programs for analysis and visualization of three-dimensional human brain funcational magnetic resonance imaging (FMRI). It can color overlay neural activation maps onto higher resolution anatomical scans. Slices in each cardinal plane can be viewed simultaneously. Manual placement of markers on anatomical lanmarks allows transformation of anatomical and functional scans into stereotaxic (Talairach-Tournoux) coordinates. Facilities are provided for several types of statistical analyses of multiple 3D functional data sets.
[*] New! AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers.
[*] ANALIZE system has features integrated, complimentary tools for fully interactive display, manipulation and measurement of multidimensional image data. It can be applied to data from many different imaging modalities, including CT, MRI, PET, SPECT, ultrasound and digital microscopy.
[*] Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Available here. The original ftp site is joplin.biosci.arizona.edu.
[*] BALSAC (Build and Analyze Lattices, Surfaces, And Clusters, (C) Copyright K. Hermann 1991-6) allows the construction, visualization, and interactive analysis of general crystal lattices including single crystal surfaces (LATTICE sessions) and of finite clusters and molecules (CLUSTER sessions). Structural information can be stored on ASCII-type data files using a variety of different formats including gray scale and color PostScript to obtain high quality print output using PostScript printers and typesetting devices.
[*] CACTVS Is a visualization package for chemist. Features:
  • A full-featured 2D structure editor (csed)
  • A 2D structure browser (csbr)
  • An Image viewer, which can also compute GIF images from connectivity alone (csimg)
  • A multi-spectra viewer (NMR, IR, UV/VIS, MS), especially useful for spectra found on the WWW (csir)
  • An NMR viewer with rather restricted capabilities
  • An structure data access/download tool for Chemical MIME files on the WWW (cswa)
  • A WWW structure database access client (csws)
  • An XY grapher for numeric information attached to structure datasets
  • A client for a database of computed NMR shieldings (cssharc)
  • A GUI-less basic client which can for example be used for computation services on the internet (via dedicated ports or as CGI program) and for command-line function testing (csts).
[CM] ChemSimphony ChemSymphony is a platform-independent set of interactive Java applets that allows 3-D molecular structures to be easily incorporated into HTML documents. The system understands most of the common file formats. The structures can be manipulated in real time, rendered in a variety of styles, and then edited by the user. There is a Lite (and free) version.
[GPL] New! chemsuite is a being developed Chemical Drawing and Simulation Software for Linux/X11. This software is in early development and when it is done it will enabled to do Monte Carlo simulation, Molecular Drawing, Molar Weight Calculation, Molecular 3D Modeling and Chemical reaction Simulation.
[*] Chemtool is a program for drawing organic molecules easily and store them as a X-Bitmap file.
[*] Cn3D Cn3D is a 3D molecular structure viewer, allowing you to visualize and rotate structure data entries from Entrez. Cn3D comes as a standalone executable program, and it is also built into Network Entrez 5.0 and up software (excepting Win16 versions). The name "Cn3D" is an abbreviation of "See in 3-D".
[*] Democritos is a set of C++ classes which have been specially written to provide support for Bioinformatics and Computational Chemistry. Although young, the basis is that they are easily extensible and also have a sophisticated navigation system.
[*] DisMol is a Java molecular browser, which enables retrieving the structures from the Internet.
[*] New! DNA/GUI (DNA Graphical User Interface) is an interactive software system for rapid and efficient analysis of images of the types used in genome mapping, such as autoradiograms and electrophoretic gels.
[GPL] DND (Dream aNd Dreamer) project intends to build a complete, user-friendly GUI of the Molecular Dynamics simulation of the molecules. DND uses GTK+ and GNOME as the GUI toolkit. It is in development.
[*] Dotter : a dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis. Dotter is a graphical dotplot program for detailed comparison of two sequences. Here, every residue in one sequence is compared to every residue in the other sequence. The first sequence runs along the x-axis and the second sequence along the y-axis. In regions where the two sequences are similar to each other, a row of high scores will run diagonally across the dot matrix. If you're comparing a sequence against itself to find internal repeats, you'll notice that the main diagonal scores maximally, since it's the 100% perfect self-match.
[*] DRAWxtl produces output files in the Virtual Reality Modelling Language (VRML) or Persistence of Vision (POV-RAY) ray-tracing formats. The VRML format can be viewed locally or across the Internet, and the viewer can rotate and/or zoom the drawing in real time. The POV-RAY form matches the initial view of the VRML object, and is used to make high resolution pictures for publication. DRAWxtl can make ball-and-stick diagrams with spheres or thermal ellipsoids. Anisotropic coefficients can be input as Uij, Bij, or betaij.
[GPL] New! Garlic is a free molecular visualization program written for unix and unix clones.
[*] New! gBioSeq is a graphical multiple DNA sequence alignment editor for GTK/Linux. It provides an easy to use interface to manual alignment, seach as SeqApp on Macintosh. Sorry, it is only available in french for the moment.
[GPL] New! Gdis is a GTK based program for visualizing molecules and periodic systems. It also acts as a GUI to other programs to offer minimization and rendering.
[GPL] New! gdpc is a tool for visualising the output files of a molecular dynamic simulation. It can be customized to read almost any input file format and animate it. It can also be configured to output images of each frame.
[*] Helena is a program that is in use at Utrecht University for data reduction of CAD4 data.
[*] Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments that have been tightly integrated with a friendly user interface to provide a robust tool for large scale physical mapping. "Image" is able to process gels from a wide variety of scanning technologies and has been tested on various fingerprinting protocols, producing normalized bands and normalized gel images as output.
[*] JChemPaint is a program for drawing 2D chemical structures. JChemPaint is far from being complete. It still needs plenty of development but you can already draw a structure and save it to (and load it from) MDL mol files.
[*] Jmol is an open-source molecule viewer and editor. It was originally intended to be a fully functional replacement for XMol, but along the way, we've tried to improve some parts of the XMol interface that we found annoying. Jmol is written in Java using the Swing GUI components. After we duplicate the functionality of XMol, we will be adding features of particular interest to the chemical community, including molecule editing, simple force-field based minimizations, molecular dynamics (microcanonical ensemble), and Langevin dynamics (canonical ensemble).
[*] KineMage (Kinetic Image) is a scientific illustration presented as an interactive computer display. Operation on the displayed kinemage respond within a fraction of a second. The entire image can be rotated in real time, parts of the display can be turn on or off, any point can be identified by picking it, and the change between differnt forms can be animated. Kinameges are proposed as a subtype of chemical MIME standard. There is an alternate KineMage page.
[*] KMol calculates elemental compositon and molecular weight of compounds from their chemical formula. KMol supports user defined groups and elements, unlimited nesting of subgroups, multicomponent compounds, global and per-user symbol definitions. It runs under Linux, and is designed to be used with the KDE.
[*] MAGE is a display program to view and explore kinemages. A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond quickly: the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be animated.
[*] MidasPlus (Molecular Display and Simulation System) is an advanced molecular modeling system developed by the Computer Graphics Laboratory (CGL) at the University of California, San Francisco. The system is used daily in university-level research programs in order to display and manipulate macromolecules such as proteins and nucleic acids. Ancillary programs allow for such features as computation of molecular surfaces and electrostatic potentials and generation of publication quality space filling images with multiple light sources and shadows. MidasPlus is distributed as documented source code to serve as both a starting point and training tool for others interested in doing their own software development.MidasPlus is licensed by the Regents of the University of California. For non-profit institutions and government agencies the cost of a MidasPlus license is $350.
[GPL] MOISS (Molecular Integration and Sampling Software). is a n-particle, n-dimensions Monte Carlo Schroedinger equation integrator. It implements multiple educational and research potentials. Our goal is to implement a freely available general purpose QMC program released under the GNU/GPL program.
[*] MOLDEN is a package for displaying Molecular Density from the Ab Initio packages GAMESS and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac. 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; tekronix4014, hpgl, postscript, XWindows, 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. 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 was also submitted to the QCPE (QCPE619) Molden3.2 can generate VRML2.0 scenes.
[*] Molecule Editor entirely written in Java You may also download the 1800 or so lines of commented java code and modify and use them for any non-commercial puposes (for commercial uses, please ask the author). Also available is the source code for the standalone version. Molecule Editor does not do anything but draw a molecule. You cannot save into a file, print or send the drawn molecule to a modelling package etc... Molecule Editor is just a molecule drawing module for some WebChem software that other people will write in the future or have started writing already.
[*] 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. See also ftp.bruker.de/bruker/MOLMOL
[*] Molscript is a program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Colour, greyscale, shading and depth cueing can be applied to the various graphical objects. You must ask to the author to obtain a free copy. See also this link.
[*] Montage is a 3D reconstruction package that allows a user to reconstruct data from serial sections in 3 dimensions on a relatively inexpensive PC with Linux. It requires little specialized hardware (only a Summagraphics bitpad) and comes with several programs for analyzing and displaying the data in 3D. Contours are traced manually, stored and displayed as polygons. A hidden-line routine allows transparency for stereo pictures.
[*] NanoCAD is a Freeware CAD System for Nanotechnology. NanoCAD is a project to put together a GNU-licensed CAD program suitable for designing and testing nanotechnological widgets. NanoCAD brings together two disciplines, computer-aided design and molecular modelling, to help people design molecules and perform dynamic mechanical testing on them.
[*] NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. Any rooting of the unrooted tree can be interactively specified using the mouse. NJplot also allows zooming, branch swapping, display of bootstrap scores and printing in the PostScript format. NJplot can therefore be used as a graphical extension of any package of phylogenetic program which employs the standard tree format for storing trees (i.e., with most such packages).
[*] ORTEP-III The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program is a computer program, written in Fortran (source code is available; the utility F2C was succesfully used to convert the code into C), for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.
[*] PADRE (Population Analysis and Duplicate Removal) is a general purpose utility that can be used to analyse the results of conformational searches, and to measure similarity and differences between molecules. Some of the highlighted capabilities include:
  • molecular overlap based on sterics and electronics
  • cluster analysis
  • Tcl/Tk based dendogram viewer interface to RASMOL
  • automatic removal of duplicates from a multi-conformer file
  • RMS distance / torsional difference measurement
  • automatic detection of topologically equivalent atoms (automorphisms)
  • support for numerous input and output file types
  • simple command line interface
[*] Platon This is a versatile crystallographic tool implementing a large variety of standard geometrical calculations (i.e. bonds, angles, torsions, planes, inter-molecular contacts (H-Bond analysis), Coordination etc), tests (i.e. MISSYM, VOIDS etc.), utilities (cell transformation, SHELXL input etc.), graphics (e.g automatic labelled ORTEP-type plots) and several filters (i.e. the DIFABS technique for empirical absorption correction (Walker & Stuart) and SQUEEZE for handling disordered solvents (= BYPASS procedure, (v.d. Sluis & Spek, Acta Cryst. (1990), A46, 194))). See also ftp://esca.atomki.hu/pub/linux/apps/chemistry/platon and the manual. Platon now includes Pluton, a program for interactive molecular graphics. It is designed for use in a crystallographic context. However, it can be used for the display and analyses of molecules in an orthogonal (Angstrom) coordinate system as well. Various hardware/software/graphics platforms are supported.
[*] Pluton is a program for interactive molecular graphics. It is designed for use in a crystallographic context. However, it can be used for the display and analyses of molecules in an orthogonal (Angstrom) coordinate system as well. Various hardware/software/graphics platforms are supported.
[*] PovChem takes three-dimensional chemical information in the Protein Data Bank format, constructs a model, and outputs a plain-text file that contains that model in the POV-Ray format. Its interface is simple: it asks the user key questions on what type of model is desired, then generates all that is needed for a basic POV-Ray scene, including camera position, lights, texture, and colors. No knowledge of POV-Ray's command language is necessary, and in fact, PovChem can be configured to call POV-Ray automatically.
[*] PROCHECK Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. The plots can be in colour, if required. PROCHECK-NMR is a suite of programs that have been derived from the PROCHECK programs to analyse ensembles of protein structures solved by NMR.
[*] Qmol Molecular Viewer for structure and trajectory data. It supports the following:
  • Display stick figure molecular structures from a PDB file (more formats are possible if there is strong demand).
  • Animate molecular trajectories stored in the DCD file format.
  • Interactively measure bond lengths, bond angles and torsion angles.
  • Display atom labels.
[*] RasMol 2.5 is a Molecular Graphics Visualization tool (by Roger Sayle). The original ftp site is ftp.dcs.ed.ac.uk. Here you can find the manual, as well as source of RasMol 2.5 ready for Linux, the executables only for Linux, the documents only (WinWord, PostScrip and txt formats), and the Windows MS-DOG version of RasMol 2.5
[*] Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, and cylinders with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware.
[*] RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
[*] Spock is a full-featured molecular graphics program. 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).
[*] Turbo Frodo is a general purpose molecular modelling environnement.
[*] Turbo X is a graphic tool that allows to model and manipulate protein and acid nucleic structures. It runs on computers with bitmap display under X.
[*] VIEWMOL programme is a graphical front end for some quantum chemical as well as for some molecular modelling programmes. It is able to visualize results of such calculations. The programme is able to show the geometry of a molecule, to trace a geometry optimization, to animate normal vibrations of a molecule, to draw IR, Raman, and inelastic neutron scattering spectra of a molecule, an MO energy level or density of states diagram, basis functions, molecular orbitals, and electron densities of a molecule and to show forces acting on each atom in a certain configuration. The structure of the molecule and basis functions, molecular orbitals, and electron densities can be plotted, the normal vibrations may be drawn as arrows into this plot (HPGL output), the spectra can be written as files suitable for LaTeX and the MO energy level or the density of states diagram can be plotted (HPGL output). All drawings can also be saved as TIFF files. Animations of normal modes can be converted to a video file (MPEG), e. g. for inclusion into World Wide Web documents (requires additional programmes available on the Internet). The programme can also be used as an interface to the freeware ray tracing programme RAYSHADE. A file containing a description of the scene for this programme may be generated and the ray tracing programme can be used from within VIEWMOL.
Actually VIEWMOL can be used with DISCOVER, DMOL, GAUSSIAN 92, MICROMOL, and TURBOMOLE outputs as well as with PDB files (VIEWMOL is therefore suited as a viewer for structural data on the World Wide Web). The programme can easily be extended to read output of other programmes.
[*] VMD (Visual Molecular Dynamics) is a program for interative display and animation of molecules. It runs on SGI, Sun, HP, IBM, and Linux workstations. It supports OpenGL and Iris GL accelerated 3-D rendering. VMD can be compiled from source for all supported platforms. Binaries are currently distributed for SGI, Sun, HP, and Linux. The program is a part of MDScope, (see Molecular).
[*] Weber's Java codes Steffen Weber's Home Page contains many Java codes that many chemists and physicists might find interesting, like: JWEISS (Java software for analizing pseudo-Weissenberg imaging plate data), JSV (Java Structure Viewer), JOR (Java Reciprocal Space Viewer), IPC (Imaging Plate Control software), JShape (Java Crystal Shape Viewer)....
[*] XBS is a simple but very useful program for plotting ball-and-sticks models of molecules or crystals under the X Window system. By displaying successive "frames" a kind of movie can be shown. The program can write Postscript output files. A nice feature (in my view) is that xbs is controlled by keystrokes and not by mousing and clicking. To run xbs, a reasonably recent X Window release (X11R5, probably) is needed, but Motif is not required.
[*] xcosm is an X-Windows interface to two Computational Optical Sectioning Microscopy (COSM) algorithms for removing out-of-focus light in 3-D volumes collected plane by plane. The interface allows users to view and process multiple 3-D datasets within a simple mouse-driven environment.
[*] XCrySDen (X-Window Crystalline Structures and Densities). Program Purpose:
  • molecular and crystalline structure render program
  • property analyzer
  • graphical user interface (GUI) for the program CRYSTAL95/98
  • yields visualization of crystalline structures, 2D/3D electron densities and generates k-mesh for band structure plots for WIEN97 program
By Tone Kokalj.
[GPL] New! XMakemol is a program written in ANSI C and using the X, Xt and Motif libraries which can be used to view and manipulate atomic and molecular data given in xyz format.
[*] 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. These can be converted to other formats using the ImageMagick image processing toolkit. Conversion between a wide variety of molecule file formats can be accomplished using a program called Babel.