Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?

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    • February 21, 2020 at 1:46 pm #3354
      Anonymous

        Hi!

        I have one protein that I would like to model ab initio the final 29 residues (1 – 160 is fixed/I have the x-ray crystallography model,  161 – 189 is the region to be modeled).

        I am using the following parameters:

        – protein.tpb

        CLAIMER RigidChunkClaimer

        REGION_FILE protein.region

        PDB_FILE protein.pdb

        END_CLAIMER

        – protein.region

        RIGID 1 160 0 0 0

        – the command I ran :

        /home/users/mimi/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/minirosetta.default.linuxgccrelease @/home/users/mimi/broker.args -in:file:fasta /home/users/mimi/protein.fasta -broker:setup /home/users/mimi/protein.tpb -database /home/users/mimi/rosetta_bin_linux_2019.35.60890_bundle/main/database -frag3 aat000_03_05.200_v1_3 -frag9 aat000_09_05.200_v1_3 -nstruct 200

        – Everything runs fine! The problem? Even specifying -nstruct 200, I only get 100 structures… Can someone please let me know what I’m doing wrong? Because I believe this is the right protocol (as far as I know at least… and as far as I’ve been reading in this forum).

        Thanks!

      • February 21, 2020 at 8:41 pm #15164
        Anonymous

          The -nstruct in your command line is probably being over-ridden by something in your flags file (args file).

          Look in the args file you specified: /home/users/mimi/broker.args  and see if there’s something like “-out shuffle_nstruct 100”

           

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