Knowledge Base

How do I generate a protein multimer structure from the monomer using the crystal symmetry?

There are several options that you can use:

Use the Protein Preparation Wizard

  1. Type the PDB ID in the text field.
  2. Select the "Biological unit" checkbox.
  3. Click on "Import" to load the structure into Maestro.
  4. Click on "Preprocess" to prepare your structure and give each chain a unique chain name.

Download the Biological Assembly from the RCSB web site

  1. On the web site, search for the PDB structure that you want to use.
  2. On the page for the structure, choose Download FilesBiological Assembly. The individual monomers are downloaded in an archive file (.gz).
  3. Extract the archive file and import the assembly into Maestro. It is imported as multiple entries, but each entry has the same chain name.
  4. Select a chain, then click on Edit3D BuilderOther EditsChange Atom Properties.
  5. Choose “Residue / Chain name” from the Property option menu.
  6. Display each entry in the Workspace, and set the chain name to A, B, C, etc. using the tools in the 3D Builder panel.
  7. Select the entries in the Project Table and choose EntryMerge.

The merged entry is a new structure containing all the renumbered chains in their crystallographically-related locations.

Use the Crystal Mates feature in Maestro

  1. Open the Maestro Preferences panel via EditPreferences (MaestroPreferences on macOS).
  2. In the section WorkspaceCrystal Mates, check “Rename crystal mate chains”. This will give each chain a unique chain name.
  3. In Maestro, go to EditCrystal Mates to generate the crystal mates.
  4. This creates a new entry including all copies that are adjacent to the original chain in the crystal.
  5. Delete the chains that are not needed.

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