Generate symmetry mates for proteins

The Symmetry Mate Editor extension in SAMSON lets you recreate symmetric replicas of proteins using transformation data found in PDB files. These replicas reveal how proteins are arranged in their crystal structures and biological assemblies - a crucial step for many protein-modeling and molecular-design workflows.

Note

PDB files often provide very interesting information on how proteins are organized in their crystal structure and biological assembly.

Adding the Symmetry Mate Editor

1. Sign in to SAMSON Connect.
2. Visit the Symmetry Mate Editor page and click Add.
3. Restart SAMSON - your extension will be ready to use.

Why Generate Symmetry Mates?

• Visualize biological assemblies from crystallographic units.
• Explore protein-protein interfaces and potential binding sites.
• Reconstruct quaternary structures for simulations and design.
• Create symmetric protein complexes or nanostructures in design pipelines.

Activating the Editor

Open the editor using either:

• Find everything: Press Shift+E and search for "Symmetry Mate Editor".
• Editors menu: Left-side viewport menu ... > General > Symmetry Mate Editor.

Once activated, control nodes appear in the viewport representing symmetry transformations.

Exploring Symmetry Mates

Use Ctrl/Cmd + mouse wheel to scale the number of visible control nodes. Here's an example with 1BRE:

Hover over a control node to preview the replica in real time.

Left-click a node to permanently generate that replica. This way, in a few clicks, you can generate a complex structure:

CRYST1 vs. BIOMT Records

The Symmetry Mate Editor supports both:

Record type	Description	Widget color
CRYST1	Symmetry from crystal lattice	White
BIOMT	Symmetry from biological assembly annotations	Yellow

You can toggle between the two using the editor's interface. Here's an example with 1B5S:

Generating All Replicas at Once

Hold Ctrl/Cmd before hovering and clicking a control node to preview and generate all symmetry mates in one action:

To preview and create all replicas simultaneously, press and hold Ctrl/Cmd before hovering and left-clicking a control node:

Applications in Molecular Design

• Build complete oligomeric assemblies from asymmetric units.
• Design symmetrical protein cages or scaffolds.
• Test how binding sites repeat across symmetry mates.
• Simulate interactions between symmetric chains in molecular dynamics.

Tips

• Use the Ribbons visual model to clearly distinguish chains. You can colorize per chain.
• Combine with Symmetry Detection to analyze axes and RMSD.
• Use Undo (Ctrl/Cmd + Z) to remove unwanted replicas.

Need Help?

Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.