To overlay a structure on an already-open structure:

  1. Open the first structure file.
  1. Choose File > Add to Document or press Ctrl/Cmd+E.

  1. In the ensuing dialog, choose the placement of the structure(s):

    • To place the center of one structure directly on top of the center of the other structure, choose Center on-screen to align similar structures.

    • To place the structures side-by-side without overlapping, choose View a large "split entry" structure or biological assembly.
  1. Within the same dialog, add or remove files from the Files area:

    • To open a file chooser and add one or more files to the list, click Add File.

    • To choose a file with a known ID from the PDB database, select Add PDB ID. The ensuing dialog is the same one used for the menu command File > Open from PDB. See Opening a PDB File When You Know the ID for more information.

    • To enter information by typing or by pasting data from the clipboard, click Enter. A pop up dialog appears. See Type or paste a protein sequence to learn how to enter the sequence in this dialog.

    • To remove a file from the list, select it and choose Remove.

Once the desired files appear in the Files area, click OK to open them in Protean 3D, or Cancel to exit from the dialog without opening any files.

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