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how to control alignment for energy_based_clustering

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how to control alignment for energy_based_clustering


I am using the energy_based_clustering application to cluster results from a protein-protein global docking job. One of the partners is kept fixed, so I would like to cluster based on the RMSD of the moving partner alone, without any alignment. I assume that the clustering algorithm is aligning the whole structure to minimize RMSD. Is this correct? If it is, is there a way to skip the alignment and calculate the RMSD directly from the input structures?

A related question is about the cluster:energy_based_clustering:chains_to_ignore flag. I want to use it so it calculates the RMSD only for the moving protein. It needs a list of chains as an integer vector, but it's not clear in what format and how to specify the chains.





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Tue, 2023-02-28 10:13