How can I view sequence variations in the context of a 3D structure?

The Multiple Sequence Viewer (MSV) makes this task relatively easy.

Load the structures/sequences under consideration into the MSV and align them. Use Color Use Color → Residue Similarity in the MSV window to shade the residues by similarity, then tweak the spectrum used by going to the Color → Adjust Color Range (Suite 2010 on) or Color → Weight Colors by Sequence Identity panel (earlier releases).

With the colors correctly configured the structure in the Maestro Workspace can be updated using the Color → Apply Colors to Workspace option.

From here you can use the normal Maestro tools to display surfaces colored by the sequence similarity (atom color) etc.

Keywords: MSV, Maestro, protein sequence identity, visualisation

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