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PyMod 2 is a PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and MODELLER). The current PyMod release, PyMod 2, has been extended with a rich set of functionalities that substantially improve it over its predecessor (PyMod 1.0), particularly in its ability to build homology models through the popular MODELLER package. Starting from the amino acid sequence of a target protein, users may take advantage of PyMod 2.0 to carry out the three steps of the homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod 2.0 may also be used outside the homology modeling context, in order to extend PyMOL with numerous types of functionalities. Sequence similarity searches, multiple sequence-structure alignments and evolutionary conservation analyses can all be performed in the PyMod 2/PyMOL environment.


PyMod 2 runs on Windows, Mac OS X and Linux versions of PyMOL. It is compatible with PyMOL version >= 0.99 and it has been tested on both unofficial and official PyMOL builds distributed by Schrodinger.


Please refer to the PyMod 2.0 User's Guide to learn how to install PyMod 2 on your system (briefly, PyMod 2 may be installed as any other PyMOL plugin, however manually installing its dependencies and external tools and configuring them may require some time, that is why we distribute easy-to-use Installer Bundles which will automatically take care of the whole installation process, see the Download link below).

How to use PyMod

A series of introductory tutorials and in-depth information about all the PyMod 2 functionalities can be found in its User's Guide.

Home page:

User's guide:

Download Installer Bundles:

GitHub page:


Janson, G., Zhang, C., Prado, M.G., and Paiardini, A. (2016). PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. Bioinformatics. PMID: 27742701