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Article ID: 488 - Last Modified: April 30, 2012

I want to cluster conformers, but I cannot find XCluster. What can I do?

In Suite 2010, XCluster was replaced by a python script called Conformer Cluster (conformer_cluster.py). 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.

If you would like to continue using XCluster/cluster, your license enables the 2009 version of the software. Set your SCHRODINGER environment variable to the 2009 installation of Schrodinger software, and continue to use XCluster.

If using the command line version, cluster, is acceptable, you may do so in Suite 2010 with the command

$SCHRODINGER/cluster -ARCH Linux-x86 jobname

with the cluster command file jobname.clu. The -ARCH option is required because the 32-bit version is the only version that you can use. As the XCluster manual is no longer in the documentation for Suite 2010, you will have to use the manual from Suite 2009 for the syntax of the command file.

Keywords: cluster, conformers, XCluster, MacroModel

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