Import Proteins

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Learn how to load protein structures into Blender using ProteinBlender.

Watch the full tutorial:

Overview

ProteinBlender supports importing proteins from:

• Local PDB or mmCIF files
• RCSB Protein Data Bank (online)
• AlphaFold Database (online)

Opening the Importer

1. Open Blender and make sure ProteinBlender is installed
2. The ProteinBlender workspace should open automatically
3. Look for the Importer panel on the right side
4. If you don’t see it, press N in the 3D viewport to open the sidebar

Import from File

Step-by-Step

1. In the Importer panel, locate the Import from File section
2. Click the folder icon to browse for a file
3. Navigate to your PDB or mmCIF file
4. Select the file and click Import
5. Wait for the import to complete (progress shown in bottom left)

Supported File Formats

• .pdb - Protein Data Bank format
• .cif / .mmcif - Macromolecular Crystallographic Information File

Import from Online Database

From RCSB PDB

1. In the Importer panel, find the Import from PDB section
2. Enter a 4-character PDB ID (e.g., 1CRN, 6LU7, 7BV2)
3. Click Fetch from PDB
4. The structure will be downloaded and imported automatically

Popular PDB IDs to try:

• 1CRN - Crambin (small protein, good for testing)
• 6LU7 - SARS-CoV-2 Main Protease
• 1ATP - ATP Synthase

From AlphaFold

1. In the Importer panel, find the Import from AlphaFold section
2. Enter a UniProt ID (e.g., P69905, Q9Y6K9)
3. Click Fetch from AlphaFold
4. The predicted structure will be downloaded and imported

After Import

Once imported, your protein will:

• Appear in the 3D viewport
• Be listed in the Protein Outliner panel
• Be centered at the world origin
• Display with default cartoon representation

Managing Multiple Proteins

You can import multiple proteins into the same scene:

1. Simply import additional proteins using any method
2. Each protein appears as a separate entry in the Protein Outliner
3. Use the outliner to select and manage individual proteins

Troubleshooting

Import Fails

• Check your internet connection (for online imports)
• Verify the PDB ID or UniProt ID is correct
• Check the Blender console for error messages

Protein Doesn’t Appear

• Check that you’re in the 3D viewport (not another editor)
• Press Numpad . (period) to frame the imported protein
• Look in the Protein Outliner to verify the protein was imported

Very Slow Import

• Large proteins (1000+ residues) may take 30-60 seconds
• Complex multi-chain assemblies take longer
• Check progress in the bottom-left corner of Blender

Understanding the Protein Structure

After import, you’ll see:

• Chains: Individual polypeptide chains (labeled A, B, C, etc.)
• Domains: Full chain domains (you can split these later)
• Hierarchy: Organized in the Protein Outliner panel

Next Steps

Now that you’ve imported a protein, learn how to:

• Update Visuals - Change colors and molecular styles
• Create Puppets - Group parts for animation

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