Is native.pdb necess for fragment_picker？

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    • March 12, 2020 at 7:57 am #3371
      Anonymous

        Hi，i want to use fragment_picker to get 3-mer and 9-mer fragment,with only .fasta and .psipred.Cause i do not have pdb file ,i remove the -in::file::s .pdb

        When i run fragment_picker,it tell me “can not read a referrence file”

        I want to know how to solve this,thank you 

      • March 12, 2020 at 12:38 pm #15211
        Anonymous

          Hello,

          Could you prove a more exact error message, and the exact command line you used?

          We generally recommend running fragment_picker via make_fragments.pl in the tools/fragments directory.

          • March 13, 2020 at 3:42 am #15212
            Anonymous

              Hello.

              my error message:

              caught exception

              File: src/protocols/frag_picker/scores/FragmentCrmsd.cc:258

              [ ERROR ] UtilityExitException

              ERROR: Can’t read a reference structure. Provide it with in::file::s flag

              my conmand line:

              :~/download/rosetta_src/demos/public/fragment_picking/BestFragmentsProtocol$ /home/advanced/download/rosetta_src/main/source/bin/fragment_picker.linuxgccrelease @flags

              and the flags file:

              # Input databases

              #-in::file::vall <Path to vall database>

              # Query-related input files

              #-in::file::checkpoint        input_files/2jsvX.checkpoint

              -in::file::fasta        input_files/2jsvX.fasta

              #-in::file::s                   input_files/2jsvX.pdb

              -frags::ss_pred            input_files/2jsvX.psipred.ss2 predA

              # Weights file

              -frags::scoring::config        input_files/simple.wghts

              # What should we do?

              #-frags::bounded_protocol    

              # three-mers only, please

              -frags::frag_sizes         3

              -frags::n_candidates        200

              -frags::n_frags            200

              # Output

              -out::file::frag_prefix        output_files/frags

              #-frags::describe_fragments     output_files/frags.fsc

              -in::file::vall                  /home/advanced/download/rosetta_src/main/database/sampling/filtered.vall.dat.2006-05-05.gz

               

              referrence:

              https://www.rosettacommons.org/demos/latest/public/fragment_picking/README

              It do not ask for a native pdb for necessary but i got a error

               

               

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