MSMS Plugin for PyMOL


The MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and displaying its results in PyMOL. Created by Hongbo Zhu < @ googlemail>, Biotechnology Center (BIOTEC), TU Dresden. Please cite this plugin if you use it in a publication.

1. Citation for this plugin:
    Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden.
2. Citation for PyMOL can be found at:


1. Download (Windows users please use;
2. In PyMOL, go to Menu → Plugin → Manage Plugins → Install... and install;
3. Obtain a copy of MSMS binary. MSMS is not included in the plugin. You can find the binary of MSMS here.
4. (optional) set environmental variables
MSMS_BIN and PDB2XYZRN to the msms executable and the script pdb_to_xyzrn shipped in the MSMS package, respectively. Only MSMS_BIN is needed for Windows users.


Tab Structure

Figure 1: Tab Structure: Specifying structure (PyMOL selection or PDB file).

Tab Structure

Figure 2: Tab MSMS Configuration: Configuring MSMS path and parameters.

Tab Structure

Figure 3: Tab Visualization: Specifying visualization parameters for surface vertices, normal vectors and mesh.

Tab Structure

Figure 4: Demonstation of the MSMS plugin (PDB: 1acb).


If you have any problem or suggestion about the plugin, please contact Hongbo Zhu < @ googlemail>.