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Symmetry detection in biological assemblies#

The Symmetry Detection extension in SAMSON finds and visualizes the axes of symmetry in protein complexes, viral capsids, and other large biological assemblies. Understanding symmetry accelerates many molecular design and protein-modeling tasks - from building coarse-grained models to setting up efficient simulations.

Why Detect Symmetry?#

  • Identify functional interfaces that repeat across symmetric copies.
  • Validate experimental structures by checking expected symmetry elements.
  • Reduce computational cost by simulating only the unique asymmetric unit.
  • Guide molecular design of symmetric nanomaterials or mutagenesis targets.

Supported Symmetry Types#

Category Supported symmetry types
Cyclic (Cn) Any order (C2, C3, ...)
Dihedral (Dn) Any order (D2, D3, ...)
Cubic Tetrahedral, Octahedral, Icosahedral

Note

The app may detect multiple symmetry groups at the same time.

Quick-Start Tutorial#

  1. Open SAMSON.
  2. Fetch (Home > Fetch) or load your assembly (e.g., PDB 3NQ4 or 1CHP or 1B4B). Note that depending on the chosen importer you might need to check an option to import biological assemblies.
  3. Launch Home > Apps > Biology > Symmetry Detection.
  4. Click Compute symmetry.
  5. Review detected groups and choose the axis of interest.

Example 1 - Icosahedral Capsid (3NQ4)#

The extension identifies the full icosahedral symmetry, displaying all 2-, 3-, and 5-fold axes. You can use this visualization to select a unique asymmetric unit before running heavy simulations.

Symmetries of 3NQ4

Example 2 - 1CHP#

For large assemblies, the app may propose one or more symmetry groups.

1CHP symmetries

Working with Multiple Symmetries#

Automatic detection may return multiple plausible symmetries - especially for large complexes.

Choosing the best group#

  1. Prefer higher-order groups with small RMSD values.
  2. Click a group to highlight its primary axis in the viewport.

For example, the 1B4B system has a dihedral symmetry of order 3 (D3):

1B4B symmetries

Specifying a Group Manually#

If you know the expected symmetry (e.g., D3 for 1B4B), pick it from the symmetry group and order drop-down lists:

1B4B with a chosen symmetry group

Exploring Axes and RMSD#

Each symmetry group can contain several axes. Expand the group to list them with their individual RMSD scores.

  • Single-click an axis -> highlights it in bold in the viewport.
  • Double-click an axis -> aligns the camera so you look straight down that axis.

Select symmetries

Tips for Better Visualization#

  • Combine symmetry axes with Ribbons or Surface visual models for clear context.
  • Color asymmetric units differently to emphasize repeats (e.g., colorize per chain).
  • Use Viewport snapshots to capture figures for publications or presentations.

Next Steps#

  • Export the asymmetric unit for focused protein-modeling simulations.
  • Design symmetric mutations or ligands that exploit the detected symmetry.
  • Apply the same workflow to nanoparticle design or other studies.

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.