I need to renumber the atoms in the binding sites of several proteins, so that I can cluster and align them. Is there a way of doing this?

If you want to renumber the atoms in the binding site of a protein to match another (similar) protein, you can use the Python script match_structure.py, available from our Script Center under "Workspace Tools: Match and Reorder Structures in One File Against a Reference Structure in Another File". You might also want to consider the Align Binding Sites tool on the Tools menu in Maestro to align the structures.

Keywords: atom number, align, cluster, Maestro

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