molBLOCKS can be installed from source code, or run inside a Virtual Machine. The second option is a convenient way of quickly testing the program without compiling it.

Installing from source code

molBLOCKS is provided as source code. For instructions on how to compile or install molBLOCKS, please consult the User's Guide or read the README file provided in the download package. molBLOCKS has been tested on Linux Ubuntu 12.04 LTS and Mac OS X (Mountain Lion, Mavericks).

Source code: molBLOCKS v.0.1 (MD5: 36d722c38bae0862dfad88661d4af3ba)

For convenience, here is a copy of Open Babel: openbabel-2.3.2.tgz (MD5: 9b0007560d9d838b40ab4ad06daf5610)

To visualize the structure of the fragments produced by molBLOCKS, you can use the freely available Marvin Sketch. Fragments can be directly copied and pasted into the main window of Marvin Sketch.

Running as a Virtual Machine

As an alternative, you can download a ready-to-go image of Linux Debian with molBLOCKS already installed here
(MD5: c341f829bdad3f372ab5039558905b32, right-click on control-click if your browser tries to open the .ova file).
You can run it in the freely available Virtual Box or another virtualization software. This is probably the best solution for Windows users.

After installing Virtual Box, double-click on the Linux image and import the Virtual Machine with standard settings. Alternatively, choose File->Import Appliance from Virtual Box menu. More information on importing a Virtual Machine can be found at

After successfully importing the Virtual Machine, start it by pushing the play button. Once booted, the molBLOCKS program will be in the molblocks directory, ready for use. A README file in the login directory explains how to run some examples.
© Dario Ghersi 2014