Diff Residues Plugin

A PyMOL plugin to quickly identify different residues between two aligned proteins in the specified ligand.

Features

• After manually aligning two proteins in PyMOL, click to select a small molecule
• Automatically find residues with same spatial position but different residue type within a specified range
• Draw individual bounding boxes and labels for each different residue
• Backbone atoms (CA, C, N, O) shown as lines, side chains shown as ball-and-stick

Installation

# Method 1: Direct run
pymol -cq << 'EOF'
run diff_residues.py
EOF

# Method 2: Copy to PyMOL plugin directory

Usage

1. Load two PDB files

   load protein1.pdb
   load protein2.pdb

2. Manually align

   align protein2 and chain A, protein1 and chain A

3. Click to select a small molecule in PyMOL GUI

4. Run the plugin

   diff_residues dist=6.0

Parameters

Parameter	Default	Description
dist	6.0	Search radius (Angstrom)
threshold	2.5	Position matching threshold (Angstrom)
obj1	auto	First protein object name
obj2	auto	Second protein object name

Generated Objects

The plugin creates and groups the following objects:

• diff_boxes - All bounding box objects
• diff_labels - All label objects
• {protein}_diff_N - Bounding box for each different residue
• {protein}_label_N - Label for each different residue

Example

pymol -cq << 'EOF'
load complex1.pdb
load complex2.pdb
align complex2 and chain A, complex1 and chain A
select Sele, complex1 and chain C and resn LIG
run diff_residues.py
diff_residues dist=6.0, threshold=2.5
EOF

Reference

This plugin is inspired by GetBox-PyMOL-Plugin by Mengwu Xiao, which provides docking box calculation for LeDock, AutoDock and AutoDock Vina.