Mario Valle Web

Free tools survey

During the CSCS User Day 2005 chemistry visualization tutorial I started collecting a list of the most used non-commercial chemistry and crystallographic visualization tools. Here is the status as today. Suggestions and additions are welcome!

Goals of this survey are:

  1. To have ready a pondered suggestion for who want to start using visualization.
  2. To collect nice and interesting ideas to be included in tools like STM4.

To be considered for this survey a tool must be:

  1. Non-commercial
  2. Multiplatform
  3. Not too old
  4. With active development and user communities

A related document collects a (disordered) list of facts and interesting things about tested tools.

At the end a list of non compliant, but popular tools has been added to not forget them.

Obviously other lists are available on the net, but my goal is much more limited and focused.



Very good tool. Slanted toward big protein visualization. Active development. Scriptable.


New version of the popular lightweight tool.


Java applet, successor of Chime. Really nice, but not a general end user tool.


BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality.

Seems fast, simple, but extensible. The examples gallery is quite impressive. The view manipulation is not so simple and definitely not interactive.


A simple viewer based on Java and Java 3D (so it is not too fast). It interfaces also with Gaussian03.


Started testing on Windows. But not yet succeeded with the installation.

[not checked]

Tested on Windows. Very contrived and old user interface and limited representation modes and input formats. Instead it seems more an integrator for analysis tools. It has a Tcl plugin functionality.

A good tutorial is available.


Graphically simple crystallographic viewer. I was able to run it only on its examples: it crashes on Windows trying to display some standard Shel-X file. Also pollute your data directories with generated files.


Not tested yet. Read conditions of use carefully.

[not checked]

Python based. Not immediate GUI. Permits sculpturing and molecule editing. Powerful.

There is a good tutorial available.


Python based environment. Extensible and visual programming based. Not too fast.

Deep View – Swiss-PdbViewer

Tested on Windows only. Very slanted toward protein analysis. Very basic representations and rendering. Personal scripting language. But otherwise the analysis functions are really powerful.

A tutorial is available.


Tested. From the graphical point of view it is really fantastic! Well, with some small annoyance (how do you center the molecule?). Has a scripting language, read all formats read by Babel, has synchronized views (aminoacid list and structure), but more advanced manipulations are reserved for the commercial version of the tool.


Not tested yet. As per January 2006 seems that the site has disappeared.

[not checked]

Tested on Linux and Mac. Seems a very powerful tool in the macromolecular area, but the user interface is not simple to use sometimes (e.g. how do you delete a created surface?). Its ability to create a summarizing surface model is unique.

RasMol and OpenRasMol

Tested RasMol on Linux: very old and limited (it is really only a viewer).


Not tested yet. But is more a post processing tool to generate high quality images for publication.

[not checked]

Not tested yet. But is more a post processing tool to generate high quality images for publication.

[not checked]

Not tested yet. Rather limited on Unix platforms.

[not checked]

Another Java applet. Very good image quality with anti-aliasing, fog and shadows. Good control on selection and rendering. Has some shortcoming (suddenly a cartoon representation appears, but there is no way to remove it).


Installed and started test on Windows. It's a monster download (305 MB!).


Not tested yet. Another Java applet viewer. It requires Java3D.

[not checked]
Discovery Studio Viewer

Tested on Linux after passing through the discouraging registration process. Seems there is no way to submit the registration form: it locks the browser!

Anyway, it is big and slow. It has good selection capabilities and some analysis tools for biomolecules, rich data model (again, based on PDB structures), unintuitive navigation.


Graphically simple crystallographic viewer. Tested on Windows. Has some interesting feature, like X-Ray diffraction computation, interface to computational code, simple atoms selection. But the user interface has some unexpected response and behavior.


Crystallographyc viewer with a set of interesting analysis capabilities. Tested on Windows only. It is the successor of VICS-II.


Powerful, but complex. It needs a time limited license. Now offers also a version for Linux and Mac.

This tool has some user interface things that helps quite a lot usability.


Not compliant, but popular tools

The following tools are popular, but for same reason does not comply with the requirements of the original list.


Not multi platform (requires an Xserver on Windows). Quite old technology. But has a simple modeler integrated based on Z-matrix.


Linux only. Quite old technology. But has some nice ideas like ground plane with shadows.


No Windows. Complex licensing process.


No Windows. Command line interface.


On windows requires a complex installation.

Modeling tools

Those are modeling tools that I have tested.


Not multi platform (requires an Xserver on Windows). Quite old technology. But has a simple modeler integrated based on Z-matrix.


Multiplatform and new. It has good potentialities, as soon as some “peculiarities” in bond computation will be fixed.


Tested on Windows only. Very unfriendly user interface and minimal quality rendering. Has an integrated minimizer for finding the molecule conformation. Good front-end to various Quantum Mechanics codes. Export to XYZ.

Really good is instead the user interface to MO (internal) computation. The IR spectra is displayed as an aid to select the correct orbital.


Specialized tools

I found the following tools interesting for some special reason like new rendering methods, interesting manipulations possibilities or for the tool implementation method. Maybe they are not tools to be used or recommended as a general purpose tool, but they can provide ideas for other tools.


Entirely new rendering method for space filling and ball-and-stick representations. This method compute almost instantaneously shadows and ambient occlusion lighting. The result convey shape and depth much more clearly than other tools.

The Ramachandran Plot Explorer

The Ramachandran Plot Explorer is not simply another protein viewer. It has been specially designed to focus solely on the φ, ψ and χ angles. With this tool you can easily:

  • explore conformation changes
  • explore secondary structure and common loop structures
  • construct and edit protein sequences interactively

Another peculiar thing is that this tool is built using an open-source games engine (allegro).


The TLSView molecular viewer specializes in visualizing TLS (translation/libration/screw) rigid body displacements in macromolecular structures.


In our research (molecular, electronic structure, and rearrangements of radical ions) there is a need for rapid inspection of the nodal properties and the general shape of MO’s from different quantum chemical calculations (e.g. selection of the active space for a MCSCF calculation).

The graphic tools implemented in GaussView, Spartan, CaChe, Hyperchem etc. visualize MO’s as three-dimensional electron density plots which take some time to calculate and do not always readily yield insight into the nodal structure of MO’s.

Other free software lists