Calibur not listing cluster members

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    • July 1, 2018 at 8:07 pm #2952
      Anonymous

        Hi,

        I generated 10,000 structures using the rosetta CM method. I then tried to cluster them using calibur in Rosetta 3.9, build# 60072 using the command “calibur.mpi.linuxgccrelease -pdb_list pdblist.txt” but it won’t display the members of each cluster. It only shows the following at the end:

        Largest 2 cluster centers: S_0445_4.pdb(35), S_0001_2.pdb(28). Margin = 20.00000%

        cluster = 0; center = S_0445_4.pdb; n_decoy_members = 35; members =

        cluster = 1; center = S_0001_2.pdb; n_decoy_members = 28; members =

        I was wondering if there was something I was doing wrong or some other way to determine the cluster members using calibur.

        I’ve attached an abreviated version of the full output in case it might help.

        Thanks in advance.

      • May 17, 2020 at 10:36 pm #15291
        Anonymous

          Hi, 

          Did you manage to sort this? I am having the exact same problem today so wondering if you found a solution?

          Thanks!

        • May 7, 2021 at 2:22 pm #15890
          Anonymous

            Hi, 

            I have also had exactly the same error, though with some extra lines. It only gives me the center of each cluster, but fails to extract the names of the cluster members. 

            The end of my output file looks like this: 

            cluster = 0; center = 43539164D2_transformed79_flexV1KIH_0112.pdb; n_decoy_members = 4; members = Warning: attempted to access the 54 element of names_ (13)!

            Warning: attempted to access the 161 element of names_ (13)!

            Warning: attempted to access the 148 element of names_ (13)!

            Warning: attempted to access the 162 element of names_ (13)!

            cluster = 1; center = 43538884D2_transformed51_flexV1KIH_0141.pdb; n_decoy_members = 4; members = Warning: attempted to access the 145 element of names_ (13)!

            Warning: attempted to access the 150 element of names_ (13)!

            Warning: attempted to access the 168 element of names_ (13)!

            Warning: attempted to access the 167 element of names_ (13)!

             

            Any help would be greatly appreciated! 

             

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