Protein Puppets

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Learn how to create and manage protein puppets for coordinated animation and manipulation.

Watch the full tutorial:

What is a Puppet?

A puppet is a collection of protein chains and/or domains grouped together. Puppets allow you to:

• Move multiple parts as a single unit
• Apply transformations to groups
• Create coordinated animations
• Organize complex multi-protein scenes

Think of puppets as “handles” for controlling multiple protein parts at once.

Creating a Puppet

Step-by-Step

1. Select items in the Protein Outliner
   • Click checkboxes next to chains or domains you want to group
   • You can select multiple items from the same or different proteins

2. Open Protein Puppet Maker panel

3. Click Create New Puppet

4. Name your puppet in the dialog that appears

5. Click OK

The puppet will now appear in the outliner with all selected items as members.

Puppet Membership Rules

• Exclusive membership: Each chain/domain can only belong to ONE puppet
• Cannot puppet proteins: Only chains and domains can be puppeted
• Cannot puppet other puppets: Puppets cannot contain other puppets

If you try to create a puppet with items already in another puppet, you’ll see an error message.

Managing Puppets

Selecting a Puppet

• Click the checkbox next to the puppet name in the outliner
• This selects the puppet’s Empty controller object

Moving a Puppet

1. Select the puppet in the outliner
2. Use Blender’s transform tools (G, R, S) or manipulators
3. All members move together

Adding Members to a Puppet

Currently, you must:

1. Delete the existing puppet
2. Select all desired items (including new ones)
3. Create a new puppet

(Future versions will support editing puppet membership)

Removing a Puppet

1. Find the puppet in the Protein Outliner
2. Click the delete (trash) icon next to the puppet name
3. Confirm deletion

Note: Deleting a puppet removes the grouping but keeps all member chains/domains.

Puppet Hierarchy in Outliner

Puppets appear in a special section at the bottom of the Protein Outliner:

Proteins
├─ Protein A
│  └─ Chain A
│     └─ Domain 1
└─ Protein B
   └─ Chain B

─── Puppets ───
└─ My Puppet
   ├─ Protein A > Chain A > Domain 1
   └─ Protein B > Chain B

Members shown under puppets are references - the originals remain in their protein hierarchy.

Use Cases for Puppets

Multi-Chain Complexes

Group all chains of a protein complex to move them as a unit:

1. Select all chains of the complex
2. Create a puppet called “Complex”
3. Animate the entire complex together

Functional Units

Group domains by function:

• “Active Site” puppet with catalytic residues
• “Binding Domain” puppet with substrate-binding regions
• “Regulatory Domain” puppet

Comparative Views

Create puppets of equivalent domains from different proteins to compare them side-by-side.

Puppets and Poses

Puppets are essential for the pose system:

• Poses save the positions of objects in puppets
• You select which puppets to include in each pose
• See Manage Poses for details

Tips and Best Practices

Naming Conventions

Use descriptive puppet names:

• “Kinase_Domain”
• “DNA_Binding_Region”
• “Full_Complex”
• “Chain_A_B_C”

Organization

• Create puppets for functional units
• Group related chains/domains
• Use puppets to simplify complex scenes

Animation Workflow

1. Create puppets for parts that move together
2. Create poses for different conformations
3. Keyframe the poses for animation

Troubleshooting

Cannot Create Puppet

• Items already in puppet: Remove from existing puppet first
• Nothing selected: Select at least one chain or domain
• Protein selected: Cannot puppet entire proteins, select chains/domains

Puppet Doesn’t Move Members

• Check that members are actually part of the puppet (look under puppet in outliner)
• Make sure you’re moving the puppet controller (Empty object), not individual members

Members Appear Twice

This is normal - members appear both in their original protein hierarchy AND under the puppet (as references).

Next Steps

Now that you understand puppets, learn how to:

• Manage Poses - Save and restore puppet positions
• Keyframe Animation - Animate your puppets

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