ResidueWalker

ResidueWalker is a PyMol plugin designed for residue-wise inspection of protein-ligand models. It is a navigation tool for PyMOL that allows users to rapidly iterate through residues, ligands, and water molecules. It provides a synchronized view between a searchable list and the 3D viewer.

Installation

1. Download and save the plugin code as a Python file (residue_walker.py)
2. Open PyMOL
3. Go to Plugin > Plugin Manager from the top menu
4. Select the Install New Plugin tab
5. Click Choose file and select residue_walker.py.

PyMOL will confirm the installation.

Activation

Once installed, the way to launch the interface is via pymol command line. Type the following command in the PyMOL console:

initWalker

Usage

Loading Data

1. Selection Input: In the "Selection" box, type the object or selection you want to inspect (default is all)
2. Filters: Toggle the checkboxes to include/exclude
   • Polymer: Proteins, DNA, and RNA
   • Small Molecules: Ligands, ions, organic cofactors, stc
   • Waters: Solvent molecules (HOH/WAT)

Load List

Click the Load List button. The plugin will automatically:

• Creat a list of residues based on the selection and checked residue types
• Show proteins/ligands as Balls & Sticks
• Show waters as Non-bonded Spheres (nb_spheres)

Navigating Residues

To navigate, simply click any residue in the list with your mouse, use the UI buttons, or press the Left/Down and Right/Up Arrow keys.