how to do cluster after low resolution protein-protein docking? I follow the manually and use docking.sc file as cluster input file for clustering, but it doesn’t work.
Is docking.sc a score file or a silent file? clustering needs either a silent file or a batch of PDBs, the scorefile alone is insufficient information.
Did it not also generate a big pile of PDB files? Use those as inputs to clustering. I don’t think the 3.1 version of docking can produce silent files; I know the 3.2 version will be able to.
yes, it generate lots of PDB files, and I used them for clustering. But I think it would be nice to cluster based on silent file. However, it seems that 3.2 is not released yet.
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