PyMod 2.0

Sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL.


PyMod 2.0 full documentation can be found in its User's Guide, which you can download from here:


PyMod 2.0 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 2.0 on your system and download its Installer Bundles from the links in the Download page.

How to use PyMod

A series of introductory tutorials and in-depth information about all the PyMod 2.0 functionalities can be found in its User's Guide.

PyMod workflow example.

Here you will find a video tutorial for the old PyMod 1.0 version. The video shows the main functions of PyMod 1.0, which have been conserved in PyMod 2.0. However, numerous other features (such as PSI-BLAST, PSIPRED, multiple chain homology modeling and quality assessment) implemented in the new release are not present in the video. We will soon release a new video showing the features of the new release.


PyMod 2.0 is distributed under the LGPL. The source code of the PyMod project is hosted on GitHub at:

If you wish report bugs or collaborate to PyMod development with new ideas and/or code, you are more than welcome. For any kind of question you can contact us.

Notes on compatibility with PyMOL

We have tested thoroughly PyMod 2.0 on as many PyMOL builds as possible. In the List of Tested Platforms section of its User's Guide, you will find a list of the PyMOL builds on which we have tested PyMod 2. We have made every effort in order to develop PyMod 2 as portable as possible and the plugin will certainly run on many other PyMOL builds. However, since there is a huge number of PyMOL builds around, there is a chance that your PyMOL build will not support the plugin. If PyMod 2 is not running on your PyMOL, please let us know, so that we may add compatibility to that particular PyMOL build.