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Article ID: 488 - Last Modified:

I want to cluster a set of conformers. How do I do this?

You can use the Conformer Cluster script ( This is found in Maestro at Scripts → Cheminformatics → Clustering of conformers.

In the Conformer Cluster panel, the workflow proceeds down the panel. First select the conformer collection and then indicate which atoms are to be used during superposition and rmsd determination. For "all heavy atoms", click the Select button and enter "not a.e H" in the ASL field and click OK.

Next click "Calculate Clustering" after choosing the linkage method. You can investigate the results with the features in the Clustering Results section. Use the Apply Clustering section to coordinate the results. The third option "A group nearest the centroid", will generate one representative structure per cluster, and place these as a group in the Project Table. The number of clusters is adjustable.

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