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Welcome to NetSci's
List of Molecular Display and Visualization Software

Notice:Statements and opinions made for the products within this listing were supplied by their owners. Network Science Corporation assumes no responsibility for the content of these listings. All product and company names mentioned in this publication are patents, trademarks, registered trademarks or servicemarks of their respective holders. The Tabular Software Listings portion of this site are Copyright © 1995/2006 by Network Science Corporated. All rights reserved.

The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.

For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.

--- A, B, C ---

 

CACTUS: a universal, networked visual chemistry data manager for computation, analysis and visualization of arbitrary chemical information.

 

ChemCraft is graphics software for the visualization of molecular structures, vibrational modes, molecular orbitals and other properties from log files produced by GAMESS, Gaussian ab initio packages.

 

chemVISION: Reads in 3D molecular structure files in many formats, renders them in a variety of styles, and manipulates them in full 3D space. You can also query the structure interactively to identify chemical, geometric, and file content information, displaying the results with color-coded labels. Use the ZOOMING magnifying glass to highlight and enlarge portions of complex structures. Transfer 3D graphics into virtually all graphics-capable Windows and DOS programs. Available from

Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, California 92805-6627 USA
Tel: (714) 634-8100
Fax: (714) 634-1999
E-mail: info@molecules.com
 

Chime is a browser plugin for display of structures.

--- D, E, F ---

 

EduChem HS Exceptional Teaching Concepts, Inc. is developing teaching tools for chemistry and science, primarily for the secondary educational market. Under the current design, the products have the potential to be used in Colleges and Universities at the entry level as well. EduChem HS consists of five independent modules:

EduChem HS efficiently covers the curricula of most high schools. It addresses chemistry (and science) in an integrated fashion. It promotes thinking skills and has various levels of difficulty. Extended EduChem Tutorials are included in a convenient HTML format. On-line help for all the modules is available at all times. EduChem HS is extremely user friendly with the text adapted to the high school audience.

Modules easily communicate with each other. EduChem HS adjusts to the student's level of ability through easy menu options, and through more sophisticated options and tutorials. It is flexible and teacher modifiable. It allows group use, and is networkable.

The full version of EduChem (Windows 95 and NT only), has the additional capability to:

For additional information, contact:

Exceptional Teaching Concepts, Inc.
100 George St., Suite A,
Hamilton, Ontario
L8P 1E2 Canada
Phone (905) 521-1579
Fax: (905) 521-2128
E-mail: info@etci.on.ca
 

Flex is a 3-D display server that displays atoms and bonds passed to it over socket connections from client programs running on the same, or different computers. Flex is available from Michael Pique, The Scripps Research Institute, La Jolla, CA 92037; Tel: 619-554-9775; E-mail: ccms-help@sdsc.edu

 

FLIMSY is a molecular graphics and analysis program. Contact Nigel Richards, University of Florida, Department of Chemistry, Gainesville, FL 326211 USA, Tel: +1-904-392-3601, Fax: +1-904-392-8758

--- G, H, I ---

GEMM (Generate, Edit and Manipulate Molecules) is an interactive molecular graphics program used at NIH. It can be used to construct, view, modify and manipulate 3-D molecular structures. GEMM runs on SGI and supports the GL library. Contact Dr. B. K. Lee, NIH, Room 4B15, Bldg. 37 Bethesda, MD 20892 USA, Tel: +1-301-496-6580, Fax: +1-301-402-1344, E-mail at bkl@helix.nih.gov

 

Geomview

  Insight II is a 3-D molecular modeling graphics program for the creation, modification, manipulation, display and analysis of molecular systems and related data. The program consists of four modules: Viewer, Builder, Docking and AMPAC/MOPAC. It is available from Accelrys.

  IRIS Explorer is a visual programming system for data visualization, animation, manipulation and analysis, designed for scientists and engineers to create applications for displaying and analyzing complex multi-dimensional datasets interactively.

The system has a programming component which developers can use for creating new applications, and a user environment in which the applications run. This dual purpose capability caters both to end users who wish to build on an existing software foundation and to application developers who wish to target specific markets effectively.

IRIS Explorer comes with approximately 200 computational modules for reading, manipulating, writing and displaying numerical data. Among other operations, modules are provided for sampling, cropping and slicing datasets. Other modules are provided for visualizing data in 1, 2, or 3 dimensions. There are approximately 40 modules for image processing, filtering, sharping and equalizing image data, and for performing arithmetic operations on image data.

Included with IRIS Explorer is a companion application for building modules. This window/menu driven application is called Module Builder or MBuilder. MBuilder utilizes a graphical user interface to help incorporate source code, (either C, C++, or Fortran) into a graphical computational module for use in the IRIS Explorer runtime enviroment.

Version 3.5 of IRIS Explorer is available for DEC Alpha/Unix, HP9000, IBM RS/6000, SGI/IRIX (6.x) and Sun/Solaris. Also Digital Alpha NT and Windows NT. For additional information, please contact

Rick Guido/Mike Modica
Numerical Algorithms Group Inc
guido@nag.com
modica@nag.com
phone: (630) 971-2337
fax: (630) 971-2706

--- J, K, L ---

--- M, N, O ---

Maestro is a state-of-the-art graphical user interface for computer aided modeling programs. It is available from Schrödinger.

  Marvin is a program that contains applets for drawing and viewing structures. It supports the display of numerous structures and works with all Java versions. The company does not provide source code, however, custom development projects can be addressed. Marvin can be previewed at http://www.jchem.com/marvin/. For additional information, contact

Ferenc Csizmadia, Ph.D.
Managing Director
ChemAxon Ltd.
Valyog u. 7, H-1032 Budapest, Hungary
http://www.chemaxon.com
Tel: +3620 9570988
Fax: +361 3875944
mailto:fcsiz@chemaxon.com

  MidasPlus is a molecular modeling and drug design support system developed by the Computer Graphics Laboratory at UCSF. The program allows real-time display of color, line and surface displays of several interacting molecules, while qualitatively monitoring the stereo chemistry. The complete model of the molecules is generated, however it is possible to view any sub-segment in isolation for clarification. Various display options are available. MidasPlus runs on SGI, DECstation 5000 (with PXG 3D graphics option) and NeXT workstations. Contact:

Norma Belfer
MIDAS Software Coordinator
Dept. of Pharmaceutical Chemistry
UCSF
513 Parnassas Avenue
San Francisco, CA 94143-0446 USA
Tel: 415-476-5128
Fax: 415-476-0688
E-mail: norma@cgl.ucsf.edu

Molecular Images is an interactive 3-D molecular graphics software package for viewing and manipulating Protein Data Bank (PDB) macromolecular files on Windows platforms. The package consists of three programs:

All the programs have context-sensitive online help as well as a printed manual.

A new 32-bit version for Windows 95 is now available and a MAC version is due this summer (sooner for those willing to beta test). For more information or a demo, e-mail misoftware@aol.com or see our web page at http://www.concentric.net/~molimage. Price: $295 commercial, $195 academic + tax, shipping and handling. Contact:

Molecular Images
4541 Hidalgo Ave
San Diego, CA 92117
Voice mail/FAX (619)483-2051.
 

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.

 

molekel is an advanced Interactive 3D-Graphics system for Molecular Sciences. The program is a molecular graphics package for visualizing molecular and electronic structure data from the output of various Chemistry Applications including GAUSSIAN 94/98, GAMESS-US, ADF and many others. MOLEKEL is a GLUT / OpenGL application and is available for UNIX, LINUX and WINDOWS free of charge.

OrbVis is an online service (http://www2.ccc.uni-erlangen.de/services/orbital/) for the calculation and visualization of molecular orbitals. The service will visualize all MOs of any reseonable structure you create. It employs a combination of a VRML2.0 plugin and a JAVA1.1 applet with many display options to control the visual appearance. System Requirements:

--- P, Q, R ---

QMol is a program designed for displaying molecular structures and dynamic trajectories. The program (and source code) is freely available and runs on both Windows 95/98/NT and Linux. The program is available at http://lancelot.bio.cornell.edu/jason/qmol.html

Features

Qmol is a program for viewing molecular structures and animating molecular trajectories. It is based on the molview demo program by Mark Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol does not try to compete with programs like VMD , MolMol , weblab and ICM, but instead opts for a fast, an easy to use user interface with a simple set of features. It supports the following:

  1. Display stick figure and space-filling molecular structures from a PDB file (more formats are possible if there is strong demand).
  2. Animate molecular trajectories stored in the DCD file format.
  3. Interactively measure bond lengths, bond angles and torsion angles.
  4. Dynamically adjust user selected torsion angles.
  5. Display atom labels.

  Quanta is a 3-D molecular modeling graphics program for the creation, modification, manipulation, display and analysis of molecular systems and related data. The program consists of several modules for specific tasks and is available from Accelrys.

 

RAsMol structure viewer for Mac, PC/Windows and UNIX systems.

  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 and shadowing. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of mixtures of ribbons, space-filling atoms, bonds, ball and stick, etc. Programs for previewing and figure composition are written for Iris workstations (GL graphics). Output modules are available for generating raster files compatible with AVS, ImageMagick, Sun and Iris display programs. Source is available free of charge from anonymous ftp: stanzi.bchem.washington.edu. Contact:

Ethan Merritt
Department of Biological Structure SM-20
University of Washington
Seattle, WA 98195 USA
Tel: +1-206-543-1421
Fax: +1-206-543-1524
E-mail: merritt@xray.bchem.washington.edu
 

Re_View is a Windows program that enables the visualization and analysis of dynamic reaction data such as conformational analysis, reaction pathways, vibrational modes, etc.

  Ribbons is designed to display molecular models as rendered images. The data required consist of atomic coordinates in PDB format and files of color coding information. Ribbons runs on SGI and Evans & Sutherland ESV workstations. Contact:

Dr. Mike Carson
University of Alabama at Birmingham
Center for Macromolecular Crystallography, 252 BHS
79 THT University Station
Birmingham, AL 35294 USA
Tel: +1-205-934-1983
Fax: +1-205-934-0480
E-mail: CARSON@UABCMC.BITNET, carson@gtx.cmc.uab.edu

--- S, T, U ---

 

Santorini is a molecular viewer tool. It can read XYZ coordinate files of atoms and display them in a 3-dimensional view. If your XYZ file contains several coordinate frames of the same bunch of atoms then Santorini can play the file as an animation. The program also allows you to calculate the radial distribution functions as well as isotropic elastic neutron scattering structure factor.

 

SciAn is a Scientific Visualization and Animation program for Silicon Graphics workstations and IBM RS/6000 workstations with the GL option. It is being developed at the Supercomputer Computations Research Institute at Florida State University with the support of the U. S. Department of Energy and the State of Florida.

UCSD MMS (Molecular Modeling System) is an interactive 3-D molecule display program which is used to represent molecules as line drawings, dot surfaces and wire frames electron density contours. Source code is included. Contact:

Steve Dempsey
University of California
Department of Chemistry
0314, 9500 Gilman Drive
La Jolla, CA 92093 USA
Tel: +1-619-534-0208
Fax: +1-619-534-0058
E-mail: sdempsey@ucsd.edu

USURFA is a program for rapid generation of smooth molecular dot surfaces on macromolecules. It is available as program number 566 from QCPE

--- V, W ---

 

Vchem is a fully functional molecular viewer that is based upon the 3 D graphics standard OpenGL and runs on Windows 95 and Windows NT PCs. A freely downloadable version is currently available from Virtual Chemistry, 7770 Regents Road #251, San Diego, CA 92122; Phone/Fax: 619-587-8699; E-mail: info@VirtualChemistry.com.

 

VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. VEGA is written in high portable code (standard C language) and can be executed on a lot of hardware systems simply recompiling the source code. The program is already tested on the following operating systems: IRIX (Silicon Graphics), Windows 9x/NT PCs, Linux, FreeBSD, NetBSD, AmigaOS, etc.

VEGA On-line (VEGAWE, http://galaxy.farma.unimi.it/vegawe) is a server-based service for all Internet users that want use the VEGA features without install it on their computer. VEGAWE can convert several file formats, add hydrogen atoms, assign atom types and atomic charges.

Dr. Giulio Vistoli
Institut of Medicinal Chemistry
Pharmacy School
University of Milan
Viale Abruzzi, 42
I-20131- Milano
Tel: +39-02-50317522
Fax: +39-02-50317565
URL: http://www.ddl.unimi.it

Visualize can display high-quality 3D renderings of molecules and surfaces, in real-time, and can also take advantage of hardware graphic accelerators (OpenGL). It can open PDB files, and display molecules using ball-and-stick, tube, vector, and CPK models. Simple operations for building molecules is included, and proteins can be built from PDB SEQRES entries. A wide variety of surfaces can be calculated, including Connolly, density contour, electrostatic potential contour, and full density plots, and rendered in different modes (dot, solid, wireframe), color spectrums, and transparencies. RHF, UHF, and ROHF energies can be calculated, including Moller-Plesset 2nd Order, GUGA Configuration Interaction energy corrections, and solvent energies (Polarizable-Continuum Model, Self-Consistent Reaction Field, and Effective Fragment Potential). Finally, the user can run Monte Carlo simulations or analytic gradient methods (such as Newton-Raphson) to find optimal geometries. A simple force field model is also included, for calculations on larger systems. Visualize runs on Windows95, 98 and NT systems. Full source code is also available. For more information and to download, visit the Website at http://www.compbio.net/downloads/visualize/index.html 0r contact Jason L. Douglas at e-mail address jason@compbio.net

 

Viewmol is a program for the visualization of outputs from quantum chemical as well as from molecular mechanics programs. Currently supported formats include Gaussian 9x, Discover, DMol/DSolid, Gulp, Turbomole, and PDB files. Properties visualized include geometry (with various drawing modes), vibrations (animated or with arrows), optimization history/MD trajectories, MO energy level diagram, MOs, basis functions, electron density. Drawings can be saves as TIFF, HPGL, Postscript, input files for Rayshade. Viewmol uses separate "input filters" to process output files. Therefore it can easily be extended to read output of other programs.

 

VMD is a new package for the graphical display and visualization of biomolecular systems

VOID (Volume Overlap, Isotopy and Docking) is a program for computing the packing defects and the tunnels that connect them in protein molecules and for attempting to predict protein-protein associations. The program examines structures from the perspective of solid geometry rather than physical chemistry. It is available as program number 617 from QCPE

  VoxBlast is a 3-D volume rendering program designed to create 3D projections from a series of images. It uses an alpha blending algorithm to create transparency effects. In addition, the user can create and apply color palettes, apply a lighting model, make 3D movies, use scripts and much more. VoxBlast can render data from many sources including MR, CAT, microscopes and voxel based molecular models. Contact:

John Kesterson
VayTek, Inc.
305 West Lowe
Fairfield, IA 52556 USA
Tel: +1-515-472-2227
Fax: +1-515-472-8131

  WebLab is a new environment for molecular simulation, computational chemistry, and computational biology. Any desktop computer with a Web browser can be used to access MSI's collection of intuitive tools through the Internet or local intranets. WebLab creates a "virtual laboratory" allowing researchers to simulate, guide, and interpret experiments faster and more economically than is possible in a wet laboratory environment. This new line of exciting products continues to grow.

WebLab Viewer, a stand-alone tool, allows researcher the ability to view chemical structures from Accelrys' extensive library of molecular graphics. The free viewer can be downloaded from Accelrys' homepage.

WebLab Gene Explorer is an interactive graphical environment for the analyses of DNA and protein sequences, as well as protein structures. From restriction analysis to virtual mutagenesis, Gene Explorer aims to satisfy the computational needs of molecular biologists with a single software environment. It helps uses focus their research on the most promising directions, hypotheses, and candidate genes.

WINMGM, is a software package for visualization, manipulation and analysis of biomolecules ( Proteins, Nucleic Acids, Lipids,...). Visualization capabilities include real-time manipulation of high-grade graphics (CPK, ribbons,...), manipulation in relative or absolute coordinates of several molecules, rendering tools providing complex representations of "workstation quality". Construction and optimization tools for peptides and proteins include systematic search using stereo-alphabet combinatorial methods, Monte Carlo calculations, side chain optimization. Analysis tools include.properties calculation such as hydrophobic/ hydrophilic or electrostatic potentials, interdistance maps, Ramachandran maps, solvent accessible surfaces... Available on PC under MS-Windows 3.1, NT and 95. The WINMGM Demo version is located at http://www.Ibanez.li/~mr/index.html

WinPDB is a Windows-based program for visulaizing PDB files. It is available at The Brookhaven National Labs site

--- X, Y, Z ---

 

Check the XMOL website.