The MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and displaying its results in PyMOL. Created by Hongbo Zhu <hongbo.zhu.cn @ googlemail>, Biotechnology Center (BIOTEC), TU Dresden. Please cite this plugin if you use it in a publication.
Citation for this plugin:
Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden.
2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE
Download msms_pymol.py (Windows users
please use msms_pymol_win.py);
2. In PyMOL, go to Menu → Plugin → Manage Plugins → Install... and install msms_pymol.py;
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.
Figure 1: Tab Structure: Specifying structure (PyMOL selection or PDB file).
Figure 2: Tab MSMS Configuration: Configuring MSMS path and parameters.
Figure 3: Tab Visualization: Specifying visualization parameters for surface vertices, normal vectors and mesh.
Figure 4: Demonstation of the MSMS plugin (PDB: 1acb).
If you have any problem or suggestion about the plugin, please contact Hongbo Zhu <hongbo.zhu.cn @ googlemail>.