Member Site Forums Rosetta 3 Rosetta 3 – General is it possbile to cluster pdb files? Reply To: is it possbile to cluster pdb files?


    > Hello:
    > I found that rosetta could cluster the PDB files generated by rosetta itself(it generate information for PDB file which would be used during cluster). I have t thousands of PDB file generated from other program, and I am wondering is it possible for Rosetta to cluster them?
    > Thank you very much.

    It doesn’t work. It is said:

    ERROR: ERROR:: Unable to open silent_input file: ‘folding.silent.out’

    I used the cluster protocol as following:

    -radius 7
    # default clustering radius is 3A
    # fiddling with the radius is the simplest way to vary the clustering
    #-input_score_filter 100
    # exclude structures above a given energy (in Rosetta Energy Units)
    #-limit_clusters 5
    # only retain largest N clusters
    # remove putative outlier from each cluster

    -silent folding.silent.out
    # the clustering executable accepts a set of pdbfiles, (-s *pdb)
    # a file containing a list of pdbfiles, or
    # a silentfile containing multiple structures
    #-native 1ubi.pdb
    # you may optionally include the native structure if it is known
    # for benchmarking purposes. It will calculate CaRMSD from native.
    -database /soft/rosetta3.1/database/
    # edit this path to point to your rosetta3 databases

    #-prefix aa
    #-path output # path where PDB output files will be written to, default ‘.’
    # if you specify a directory name here, it must exist
    #-nooutput # suppress output of pdbfile structures

    -mute # don’t show timing info