DSSP PyMOL Plugin Manual

Introduction

The DSSP PyMOL Plugin allows users to run mkdssp directly within PyMOL and load the resulting secondary structure data from the CIF file into the PyMOL workspace.

Installation

1. Prerequisites:

   • Ensure mkdssp is installed and accessible from your system's PATH.

     Citation :
     Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637. doi: 10.1002/bip.360221211. PMID: 6667333
     

   • Have PyMOL installed on your machine.

     Citation : (Schrödinger, LLC 2015)

2. Plugin Installation:

   • Save the plugin script (dssp_cif_plugin.py) to the $PYMOLPATH/modules/pmg_tk/startup/ directory.
   • Alternatively, you can place it in any directory where PyMOL sources plugins.
   • Or you can use the Plugin Manager of Pymol.
   • Start PyMOL. If it's already running, source the plugin using:

     run /path/to/dssp_cif_plugin.py

Usage

1. Command: in pymol execution window

   run_dssp_and_load [selection]

   Replace [selection] with the desired protein object or any valid PyMOL selection. If no selection is provided, it defaults to processing all loaded structures.

2. Output: After execution, a new object named "dssp_output" will be loaded in PyMOL containing the secondary structure information from DSSP.

Workflow Example:

1. Load a protein structure into PyMOL:

   load example.pdb

2. Use the plugin to run DSSP and load the secondary structure:

   run_dssp_and_load example

3. Visualize the "dssp_output" structure to see the secondary structure annotations from DSSP.

Troubleshooting:

• Error while running mkdssp: Ensure mkdssp is installed correctly and accessible from the system's PATH.

• Permissions Issue: The plugin creates temporary files in the /tmp/ directory. Ensure you have write access to this directory.