PDB B-factor Coloring Tool

📁 Structure & Data Files

PDB Structure File

🧬

Drop your PDB file here

or click to browse

Upload your protein structure file in PDB format

Values Data File

📊

Drop your data file here

Excel, CSV, or TSV format

Two-column format: Position (1-based) and corresponding values

⚙️ Configuration

Target Chain

Chain identifier to color (e.g., A, B, C)

Offset (UniProt position − Structure position)

Enter the offset calculated as: first residue’s UniProt position − first residue’s PDB position.
Example: If the first residue in the PDB chain is residue 3, and its UniProt position is 5, enter 2.

💻 PyMOL Coloring Tip

After downloading your processed PDB, you can color it in PyMOL using the B-factor values with the following command:

                spectrum b, blue_white_red, chain A
                show cartoon

Replace A with your target chain identifier. For more spectrum commands, check out PyMOL Spectrum Wiki.