How do I align independent chains in two or more protein structures?

You can use the Protein Structure Alignment feature in Maestro, which is on the Tools menu. It uses the sequence and the secondary structure to perform the superposition. The default is to align all residues of all the proteins that are included in the Maestro Workspace.

If you'd like to only align a subset of the structures, then you will need to indicate this with an ASL expression of the form

((entry.id 1 ) AND (chain.name A)) OR ((entry.id 2) AND (chain.name B))

Here is the procedure:

1. Choose Tools → Protein Structure Alignment
2. Click Select, to open the Atom Selection dialog box.
3. Click on the Entry tab. At this point you can use either Entry name or Entry ID. Note the name or ID of the structures of interest.
4. With that, and the knowledge of the chain names (Chain tab), construct the ASL as above, based on the values for your structures. Alternately, you can copy the line above, and change the values based on your structures. Copy the ASL expression into the ASL text box. The "Show markers" feature will give a visual clue of which atoms are selected. When it looks correct, click OK.
5. Back in the PSA panel, click Align, and the results should be returned in the panel and the Workspace.

Keywords: Maestro, protein structure alignment, superposition

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