Knowledge Base

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 rcsb.org web site, search for the PDB structure that you want to use.
2. On the page for the structure, choose Download Files → Biological 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 Edit → 3D Builder → Other Edits → Change 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 Entry → Merge.

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 Edit → Preferences (Maestro → Preferences on macOS).
2. In the section Workspace → Crystal Mates, check “Rename crystal mate chains”. This will give each chain a unique chain name.
3. In Maestro, go to Edit → Crystal 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.