I have 6 protein structures aligned and I want to emphasize the amino acids that are different. How can I do this without having to go through all six sequences and coloring each residue manually?

The Multiple Sequence Viewer (Tools menu) is able to color structures and sequences in many ways, including by homology or identity.

If you did the alignment in Prime, you should see the sequence alignment in Structure Prediction panel with conserved residues easily identified.

Keywords: sequence alignment, color , residues, Maestro

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