January 3 - 6, 2001 (& cont.)
Mage and PreKin
Swiss PDB Viewer
HyperChem is a commercial molecular modeling program for Windows that is easily accessible to beginning students. It includes molecular mechanics using several force fields, together with semi-empirical and ab initio quantum mechanical calculations. Molecules may be presented as stick, ball and stick, space-filling, or dotted surface models. Molecular orbitals may be displayed as two-dimensional contour maps or as three-dimensional isodensity surfaces. UV and IR spectra are presented as spectral displays and individual vibrational modes are animated. Hyperchem reads PDB (ENT) files as well as its own HIN format files. One of the strengths of Hyperchem is that it can be driven with internal scripts as well as DDE/OLE interaction with other Windows programs. A freely-distributed web browser plug-in supports manipulable 3-D views of molecules generated by Hyperchem.
Hyperchem is available in both a standard and a "lite" version (Windows only) from Hypercube, Inc. Academic pricing is available.
Spartan is a commercial molecular modeling program similar to Hyperchem, but with stronger links to other computational programs such as Gaussian and Jaguar. The molecular editor and the computational packages are separate programs rather than a single program as in Hyperchem. Computations and displays are similar to hyperchem except that Spartan provides very nice isosurfaces painted with electrostatic potential.
Spartan is available in "plus" and "pro" versions for both Windows and Mac from Wavefunction, Inc. Network and workstation (Unix) versions are also provided. Academic pricing is available.
PCModel is a another molecular modeling package for Windows, Mac, Linux or IRIX. PCModel employs a host of force fields and allows users to modify existing force fields or create their own. PCModel does not have ab initio calculations, but creates input files for Gaussian, Mopac, Macromodel, Sybyl and other well-known packages. PC Model is available from Serena Software.
Gaussianis the "industry standard" for ab initio molecular computation of energies, molecular structures, and vibrational frequencies -- along with numerous molecular properties that are derived from these three basic computation types -- for systems in the gas phase and in solution. Additional basis sets and computation types are constantly being added.
Gaussian is available in Windows, workstation, and parallel versions from Gaussian, Inc. Academic pricing is available.
Gamess is a widely-used, freely-distributed ab initio molecular structure package developed and maintained by the members of the Gordon research group at Iowa State University. Gamess is available for many systems: source code for Unix and Linux; PCGamess for Windows; PCGamess for Linux; Gamess for ChemOffice (Cambridge Software); MacGamess for Macintosh.
Jaguar is an extremely fast ab initio electronic structure software package that provides chemical accuracy for realistic systems in reasonable time by computing portions of the molecule using ab initio methods and other portions using semiempirical methods. Jaguar is much more accurate than semiempirical methods and is much faster than other ab initio methods. Jaguar is available for various versions of Unix and Linux from Schrödinger, Inc.
We have one copy of Jaguar available at Etown -- see Neysa Nevins.
Macromodel, a molecular modeling software package from Schrödinger, Inc., allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations. Energy calculations use MM2*, MM3*, AMBER*, OPLS*, OPLS-AA, AMBER94, or MMFF (Merck-Molecular) force fields, and an analytical GB/SA continuum treatment for solvation. Energetic processes are monitored interactively by MacroModel and can include multiple simultaneous tasks. Energetic calculations may be carried out on full structures or substructures prepared with the MacroModel substructure editor.
We have one copy of Macromodel available at Etown -- see Neysa Nevins.
WebMO is a World Wide Web-based interface to computational chemistry packages. WebMO is available for free and can be installed on nearly any unix or Linux system. A three dimensional structure is submitted for computation using a true 3-D editor, via Java technology. A computational engine is chosen (currently Gaussian 94/98, MOPAC, and GAMESS are supported) and the job is submitted for computation. After the job is completed, the results of computation can be viewed without ever leaving the web browser. In addition, WebMO allows full control of a job, including queuing, killing, and the import of existing computational chemistry jobs. Support, license, and download information, and a working demo are available from the WebMO Home Page at Hope College.
ArgusLab is a complete molecular modeling system for platforms running Microsoft Windows operating systems. ArgusLab contains an interactive 3D molecule builder that allows the user to build and manipulate complex molecular structures. ArgusLab also contains a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties. Descriptive information and download are available from Planaria Software.
RasMol is a free program which displays molecular structure. It is available for on PC/Windows (RasWin), MacIntosh (RasMac), unix, and VAX VMS (the latter two via X-windows), and also (through ports by users) for NEXTSTEP and for Acorn Archimedes RISC OS. RasMol is a powerful educational tool for showing the structure of DNA, proteins and smaller molecules. It is also a powerful research tool. It is easy to use and produces beautiful, space-filling, colored, 3-dimensional images (see the Gallery!). It is the generous gift to the scientific public of its author, Roger A. Sayle, Ph.D., GlaxoWellcome, and the University of Edinburgh (all in the United Kingdom). [from Eric Martz's RasMol home page]
RasMol is supported in several versions at several locations:
The OpenRasMol site is provided courtesy of Bernstien + Sons, Information Systems Consultants.
Eric Martz at the UMass maintains a Rasmol Home Page with many useful pointers, galleries, and extensions.
A reference manual is available at UMass.
Chime is a free program to show molecular structure in three dimensions. Its images look like RasMol's because Chime is derived, in part, from RasMol. Chime differs from RasMol in that Chime sits directly on a web page (runs inside your browser as a plug-in), whereas RasMol is a standalone program (runs outside your browser as a helper program). Chime also differs in that most Chime websites show only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file. Important for web-delivered instruction, Chime can be "driven" by scripts and programs.
The UMass Chime Resources illustrate what Chime is cabable of, document Chime, and make it easier to develop Chime presentations.
Edward O'Niel and Charles Grisham (Univ. of VA) provide a fine example of on-line instruction using Chime in their Interactive Biochemistry.
Wayne Anderson and Arlen Viste have provided an interactive chime interface to some inorganic solid state structures.
Chime can be downloaded from the web site of its creators, MDL Information Systems, Inc. See Chime: Browsers, Platforms, Installation, Troubleshooting .
Chime's ability to support educational resources has had a large impact on stuctural biochemistry education, as exemplified by the many excellent resources indexed in the World Index of Molecular Visualization Resources.
An ongoing discussion of technical issues about Chime may be seen in the history of the RasMol email list.
[Some of this information on Chime adapted from Eric Martz: http://www.umass.edu/microbio/chime/whatis_c.htm]
Protein Explorer is a RasMol-like interface implemented in Chime, but Protein Explorer can offer much greater assistance and automation (see comparsion). Thus, the Protein Explorer can make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than RasMol, even for experts. Protein Explorer supports nearly* all RasMol commands, plus additional Chime-specific commands. However, Protein Explorer version 1.72 Beta is much easier to use, and considerably more powerful than RasMol. Much exploration can be accomplished without learning any of the command language common to RasMol and Chime. The main goal is for novices to be able to concentrate on the molecular structure, not on the software required to see it. [Eric Martz, Jan. 1999]
Protein Explorer vs. RasMol. The goal of Protein Explorer is to enable you to focus on the science, not the software. Chime adds a great deal of power to RasMol, but using the full power of either program requires advanced technical knowledge and a lot of time -- hence their power is inaccessible to most of the people who could benefit from it. The goal of Protein Explorer is to make the power of Chime accessible to students, educators, and scientists. More is available about the evolution of the uses of Chime and the purpose of Protein Explorer. [by Eric Martz, August 29, 2000 ]
See the Protein Explorer Homepage for registration and downloading.
Mage and PreKin A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared in order to better communicate ideas that depend on 3-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program called MAGE. A utility called PREKIN makes a starting kinemage from a PDB-format coordinate file which can then be modified on-screen in MAGE or off-line in any text editor. [Richardson: http://kinemage.biochem.duke.edu/website/kinhome.htm]
David and Jane Richardson's Official Kinemage Home Page at Duke University provides pointers for downloading MAGE and PREKIN, a tutorial on making kinemages, as well as examples and freely-available kinemages. [The MAGE and PREKIN programs are also available at Etown. Follow the links from the "MoleCVUE Meeting" folder on the desktop.]
The Richardsons have published a CD "Kinemage Supplement" to Carl Branden and John Tooze's "Introduction to Protein Structure," Garland Publishing, 1999 [available at Etown from the "MoleCVUE Meeting" folder on the desktop].
Swiss-PDB Viewer (now called Deep View) is stand-alone program for Windows, Mac, SGI, and Linux for superimposing several proteins in order to deduce strucural alignments and comparision of active sites. The viewer is tightly linked to Swiss-Model, the ExPASy (Expert Protein Analysis System) proteomics server at the Swiss Institute of Bioinformatics. The viewer integrates various modelling tools, can rread electron density maps, and can generate command files for popular energy minimisation packages. Free Download, a users' guide,a tutorial, and a gallery of stunning images is available from the Glaxo Wellcome Experimental Research page
Deep View can also be downloaded from the ExPASy Molecular Biology Server. This site also has a wealth of other materials for biochemistry and molecular biology. Extensive Deep View Tutorials are also available at this site, but the best way to get started with the program is through a basic tutorial written by Gale Rhodes from the University of Southern Maine.
POV-Ray scenes can be generated from the current view in order to make quality, ray-traced images. An example can be found here.
OpenMol is an integrated program for electronic structure and property calculations of molecules. The concept of OpenMol is based on the fundamental ideas of two software concepts: the (rule based) expert system and the abstract data type model. These together lead to the syntheses of knowledge engineering and numerical data processing and give birth to intelligent software. The OpenMol Quantum Chemical Software Package is supported by the OpenMol Community.
gOpenMol is a graphical user interface to the OpenMol programs. It runs as a stand-alone program under Windows/Linux/OSF1/OpenGL(SGI) and as a browser helper application. gOpenMol can be scripted with Tcl/Tk. A description of gOpenMol, together with a Users' Manual, links to several tutorials, a collection of utility tools (mainly for interaction with other programs), and a picture gallery are maintained by Leif Laaksonen at the Center for Scientific Computing, Espoo, FINLAND.
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. The program runs on UNIX and Windows NT/95/98/2000 and is freely available. A more detailed introduction is given on the page originally created for the BRUKER web site. The home page is There also is a (very dated) official project description. A hypertext version of the manual is available as are a tutorial and a gallery of nice images created with MOLMOL.
Gauss View is a full-featured graphical user interface for Gaussian 98 (Unix or Windows). With the molecule building facility one can quickly and efficiently construct molecular systems. Gaussian calculations can be initiated and monitored from the GaussView and when a calculation has completed, you can use GaussView to examine a variety of results graphically via its advanced visualization facilities. Gauss View is available from Gaussian, Inc. Academic pricing is available.
Molekel is a freely-distributed interactive, three-dimensional molecular graphics package designed and developed at University of Geneva and CSCS /_ ETHZ by Peter F. Flükiger. MOLEKEL is pretty much platform independent.The program is written in C/C++ and uses the OpenGL / Mesa, GLUT and GLUI libraries.The OpenGL or Mesa 3D graphics library is available on many UNIX systems, LINUX and also on WINDOWS. It represents molecules as wire frame, stick, ball-and-stick, and space-fill representations; it calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals and animates vibrational modes.It accepts PDB and XYZ coordinates and input from Gaussian, Games, and other packages and saves pictures in RGB and TIFF formats. More details are available from the home page in Geneva from which the program can be downloaded and a gallery of pictures and an on-line manual are available.
VMD (Virtual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. 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 uses OpenGL to provide high performance 3-D molecular graphics.
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.
VMD supports computers running Unix or Windows, is distributed free of charge by the Therortical Biophysics Group at Univ. of Illinois and includes source code.
WebMol II is a multi-platform, Java-based 3D viewer for protein structures. Works best with version 3.0x of Netscape or Internet Explorer. Support for Java in version 4.0x of these browsers has not yet stabilized. When using a version 4.0x broswer, the viewer may or may not function correctly depending on your particular platform and browser version. Review examples and download from WebMol II Homepage at Univ California San Francisco.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis and is downloadable from the Open Science Project. Users are encouraged to modify it to fit their needs and to contribute their changes to the project. JMol is complementary to JChemPaint, a molecular drawing tool.
MolDraw -- a molecular graphics program from the Physical Chemistry Group at the Univ. or Turin. See the MolDraw Homepage for a complete description with examples and free download. Macintosh Link (at Tetrahedron Computer Methodology/Univ. Paris)
T3D and its predecessors VoxelBox and Slicer are volumetric rendering programs. These renderings use volumetric data (which can be generated from Gaussian, for example) according to user definable color maps including gamma (transparency). Such renderings are very nice for electron density, i.e., atomic and molecular orbitals. Some examples are in the "MoleCVUE meeting" folder on the desktop. Unfortunately, T3D is currently available only through Research Systems, Inc. as part of the Noesys package which also includes Noesys (a multi-purpose front end), Transform (raster images, surface plots, contour plots), and Plot (line, scatter, double-y and parametric plots) which makes the whole thing a bit pricey.
Some sample plots of atomic orbitals using VoxelBox are available at \\Albert\courses\Chem 343\ATOMORBS\VOXELBOX\VOXELBOX.EXE
POVRay is a ray-tracing program for realistic rendering of solids (such as molecular or orbital isosurfaces).
COSMOtherm (from COSMOlogic) is a program for the quantitative calculation of solvation mixture thermodynamics based on quantumchemistry/COSMO results. The Theory and Background of COSMOtherm are presented on COSMOlogic's homepage, but it is not clear how or at what cost the program is available.
COSMOtherm is able to generate VRML files for the visualization of the screening charge density s on the molecular surface. This gives a very vivid picture of the molecules, showing the local positions of strongly interacting sites. Even details like lone-pairs are well resolved. Note, that s is a much more local and detailed property compared to electrostatic potential (ESP).
The visualization makes use of the VRML file format. Thus you need a (free) VRML viewer as a plug-in for your Browser. One of them (Cortona) can be found at: www.parallelgraphics.com/downloads.
Wayne Anderson's Crystal Viewer. An interactive crystal viewer developed by our own Wayne Anderson which allows one to set unit cell parameters, number of unit cells to be displayed, layers, viewpoints, etc.
Wayne Anderson and Arlen Viste's Interactive chime interface to some inorganic solid state structures.
Crystal Office is a Windows suite designed to create and visualize crystals and access space group information. It includes three programs: Crystal Builder, Space Group Tables, and Crystal Presentation. Crystal Builder accepts XYZ, CIF, and PDB formats. Space Group Tables features position, symmetry and reflection tables for all 230 space groups. Crystal Presentation features 2-D and 3-D WYSIWYG editing with full OLE support. Crystal Office was available from Atomic Softek (but this company seems not to be on the web now).
XtalView is a GUI software package for protein crystallography. It uses an X-windows interface on a number of UNIX platforms - SGI, SUN, DEC and LINUX are all supported from a single sourcetree. It is supported and distributed by CCMS at the San Diego Supercomputer Center. Version 4 should be available by the time you read this. XtalView is used for solving structures by MIR or MAD, for de novo model building, fitting between refinement cycles and modeling. Much of XtalView is covered in the book "Practical Protein Crystallography", McRee and Israel , McRee99 . A complete description, an online Users' Guide, and online help are available through CCMS.
Cambridge Crystalographic Database, a development of the Cambridge Crystallographic Data Center, contains X-ray and neutron diffraction analyses of carbon-containing molecules having up to 1000 atoms (including hydrogens). Molecules include organics, compounds of the main group elements, organometallics, metallic complexes, peptides up to 24 residues, mono-, di- and tri-nucleotides. The CSD reflects the published literature, is fully retrospective, and is updated on a current basis. Access is from local CD as authorized by payment of an annual fee. Academic pricing is available.
Searches are conducted and results are viewed through the Windows interactive graphical interface Conquest. A pointer to Conquest is in the MoleCVUE Meeting folder on the desktop.
Other products available from the CCDC are Isostar and Relibase. Isostar is included with a CSD license and Relibase is free of charge. Isostar allows one to gain insight into non-bonded interactions between a variety of chemical groups. For more info click here. Relibase is a program for searching protein-ligand databases.
JCE Crystallography Collection contains ToolBook tutorials contributed by Marge Kastner (Bucknell Univ.) These include:
Point Group Identification: includes introduction to point group symmetry, symmetry elements, and symmetry nomenclature.
Crystallographic CourseWare: contains 12 modules including crystal growth, symmetry, unit cells and asymmetric units, reciprocal space, precession photographs, scattering factors, thermal parameters, fractional coordinates, special positions.
This collection is available from Journal of Chemical Education Software (Special Collection 26).
Diamond is an MS Windows application for the exploration and drawing of crystal structures. It features high data capacity and a wide range of functions beginning with the generation of molecules reaching up to the construction of rather complicated inorganic structural frameworks. A trial version (current version number is 2.1d) is available free-of-charge and can be downloaded
Isis/Draw is a freely-available, chemically intelligent drawing package from MDL Information Systems for Windows and Macintosh. You can insert your ISIS/Draw sketches into documents, Web pages, spreadsheets, and presentations. You can also use ISIS/Draw to create structures to register into 2D and 3D molecule, polymer, and reaction databases, and to create queries for searching these databases. A 3D plug-in is available for download.
Chem Draw andChem 3D are two components of Cambridgesoft's Chem Office. The other main component is Chem Finder (a data base of structures and drawings). The following description of Chem Draw is from Cambridgesoft's home page:
"ChemDraw, long regarded as the ultimate chemical drawing program, advanced to new heights earlier this year with the release of ChemDraw Ultra 6.0. Among its highlights were multi-page documents, stereochemistry display and recognition, structure-spectrum correlations in ChemNMR, right-button context menus, and interactive structure-checking (see the ChemDraw 6.0 articles in ChemNews.Com 10.1 and 10.2). Nearly all of the core drawing features making up ChemDraw Pro have been incorporated in the ChemDraw 6.0 Pro Plugin.
"The new 6.0 release of Chem3D adds an integrated interface to the GAMESS electronic structure calculation program. Now Chem3D Ultra serves as the set-up and control platform for both GAMESS and Gaussian. Note that GAMESS and Gaussian must be obtained separately. GAMESS can be obtained at www.msg.ameslab.gov and Gaussian is available for purchase at ChemStore.Com. New property servers have been added to enable Chem3D to fill out property tables in Excel spreadsheets which can be analyzed to search for structure-activity relationships (SAR). Read more about this facility, called ChemSAR, in ChemSAR: An Excel Add-in in ChemNews.Com 10.3."
JChemPaint is a Java 2 program for drawing 2D chemical structures like those found in most chemistry textbooks. The program is developed as an Open Science Project and released under GNU Lesser General Public License (LGPL). The code should be considered alpha quality, but there are enough features implemented to get an idea about where the program development is heading. JChemPaint is intended to be complementary to JMol, a visualisation and analysis tool for 3D molecular structures intended to be a Rasmol/Chime replacement. (Download JMol )
JChemPaint is developed by Christop Steinbeck, Egon Willighagen, Stefan Krause and others and hosted by the Chemical Information group at the Max Planck Instiutute of Chemical Ecology. People are sought to join the development of JChemPaint. JChemPaint is associated with the OpenScience project and the 3D molecular viewer JMol, both initiated by Dan Gezelter at the University of Notre Dame .
Win GX is a graphical user interface which integrates many standard crystallographic programs including programs for:
Diffractometer file conversions (Nonius CAD4)
Model setup, unit cell specification and transformations
Data reduction (PROFIT, DREAR, LAZYPULVERIX)
Absorption corrections (analytical with several geometries, PSI-SCAN, CAMEL JOCKEY, DIFABS (sssssh!))
Structure solution (DIRDIF, SHELXS, PATSEE, SIR)
Structure refinement (SHELXL)
Maps (Fourier, contour)
Graphics (Cameron, Ortep3, Pluton, Struplo, Raster3D, RasMol, POVRay, VRML viewer)
Analysis (Thermal and other)
Publish (CIF, PostScript)
Utilities (file conversions, BABEL)
The package is freely available (with registration) from
Blackboard is a web-based course delivery system similar to Top Class and WebCT (which we have examined before). Elizabethtown College (together with Messiah, Lebanon Valley, and Susquehanna) has settled upon Blackboard. Neysa and I expect to prepare an "Atomic and Molecular Structure" unit (using MoleCVUE materials and methods) to be used as a Preparation for Organic and Biochemistry beginning fall 2001. You may experiment with this system by logging in as user: ranck with password: molecvue. Explore the course "MoleCVUE" (as yet empty) as instructor, noting especially the facilities available in the "control panel." The "Resource Center" with links to (an as yet limited set of) copyrighted materials is a developing concept which should soon be extremely useful to all of us.
Tcl &Tk Tcl (Tool Command Language) is used by over half a million developers worldwide and has become a critical component in thousands of corporations. It has a simple and programmable syntax and can be either used as a standalone application or embedded in application programs. Best of all, Tcl is open source so it's completely free.
Tk is a graphical user interface toolkit that makes it possible to create powerful GUIs incredibly quickly. It proved so popular that it now ships with all distributions of Tcl.
Tcl and Tk were created and developed by John Ousterhout. Developers all over the world followed his example and built their own Tcl extensions. Today, there are hundreds of Tcl extensions for all manner of applications.
Information, downloads, references, etc. from the Tcl Developer Exchange.
Mol2Mol is a molecule file conversion, manipulation and utility program available from Interware The current version of Mol2Mol recognizes, and interconverts more than 30 different file formats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Multiple-to-multiple multiple-to-many conversions. Calculation of pyramidalities, ring puckerings. Follow these links to a full description and trial download.
MolScript is a Unix (SBI) program from Avatar Software for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures. The user supplies an input file (the script) which specifies the coordinate file and what to render. The user has a high degree of control over the exact appearance of the graphical objects. There is now a program MolAuto, which produces a good first-approximation input file from a coordinate file.
The standard output file formats are PostScript,Raster3D and VRML 2.0. Depending on your computer system, and your installed libraries, MolScript also has an OpenGL interactive graphics output mode, and can create images in several different image file formats: SGI (aka RGB), Encapsulated PostScript (EPS), JPEG and PNG.
See the MolScript homepage for more detail.
SHMO is an interactive (Java) web program to perform electronic structure calculations within the Simple Huckel Molecular Orbital approximations. It is executable from U. Calgary. or you can obtain a copy for your server.
AIM2000 University of Bielfeld implementation of Bader Atoms-in-Molecules analysis. Determines critical points, molecular graphs, and presents contour, gradient field, and relief plots (with or without BCP's, IAS's) of rho and the Laplacian of rho. A bit buggy, but the best available at the moment. Available from AIM2000 site at Bielfeld
MORPHY98 Popelier's program for the topological analysis of electron distribution (AIM). A DOS program. Input is "card" file (like Gaussian). Uses Rasmol for fast, manipulable display. Obtain from Prof. Popelier.
WEBLAB Viewer a versatile molecular viewer from MSI (now Accerrys). Quoting from the homepage: "WebLab Viewer combines state of the art molecular graphics with a full range of Windows desktop integration tools. Using the ViewerPro, you can easily visualize and share molecular information, build molecular models, and analyze organic and inorganic structures, proteins, DNA/RNA, and crystals. This software is ideal for commercial scientists, academic researchers, educators, and students. MSI's leadership in chemical modeling and simulation has been brought to the desktop with the WebLab Viewer." Obtain from http://www.accelrys.com/weblab/viewer/index.html