Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)

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    • September 23, 2019 at 10:24 am #3263
      Anonymous

        Dear Friends, 

         

        I am running ab initio rosetta run using openmpi:

          


        
mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1.log &

         

        I see “score.fsc” file in the folder with 2000 models, and generated a RMSD vs Energy plot, whcih gives me this (the attached plot)

        All 2000 models have 0.00 RMSD, is this normal? Do I need to wait for the models to converge? your commensts and solutions are very welcome. thanks

      • September 23, 2019 at 2:29 pm #14983
        Anonymous

          Hello,

          I cannot be sure without seeing your ‘options’ file, but it looks like to me you haven’t added the flag: 


          
-in:file:native {my_native_pdb_file}

          which gives rosetta a structure to calculate an RMSD against.

          if that isn’t the case, please paste your options file here!

          • September 23, 2019 at 2:47 pm #14984
            Anonymous

              Thanks! there is no template pdb as it is a de novo structure prediciton. My options file is:

                


              
# Make sure all variable names have been replaced with absolute path and that no line begins with a $ or ~s
              
-in
              
-file
              
-fasta sequence.fasta         # protein sequence in fasta format
              
-frag3 t001_.200.3mers  # protein 3-residue fragments file
              
-frag9 t001_.200.9mers  # protein 9-residue fragments file
              
-abinitio
              
-relax
              
-increase_cycles 10     # Increase the number of cycles at each stage in AbinitioRelax by this factor
              
-rg_reweight 0.5        # Reweight contribution of radius of gyration to total score by this scale factor
              
-rsd_wt_helix 0.5       # Reweight env, pair, and cb scores for helix residues by this factor
              
-rsd_wt_loop 0.5        # Reweight env, pair, and cb scores for loop residues by this factor
              
-relax
              
-fast   # At the end of the de novo protein_folding, do a relax step of type "FastRelax".  This has been shown to be the best deal for speed and robustness.
              
-out
              
-nstruct 50000  # how many structures do you want to generate?  Usually want to fold at least 1,000.
              
-file
              
-silent abrelax.out # full path to silent file output
              
-silent_struct_type binary      # we want binary silent files
              
-scorefile score.sc
              
-overwrite      # overwrite any existing output with the same name you may have generated
              
-nstruct 50000

              Please let me know about your suggestions. Thanks.

            • September 23, 2019 at 4:24 pm #14985
              Anonymous

                Rosetta can’t give an RMSD if you don’t give it a structure to RMSD against.  RMSD is relevant when you have a “correct structure” to compare to (meaning, for benchmarking purposes).  If you are doing an unknown protein it’s not a useful metric here.

                After generating models you can do a second-pass re-scoring calculating RMSD against the best model.  If that score versus RMSD plot shows a funnel it’s a good sign that the model is correct.

              • September 23, 2019 at 4:43 pm #14986
                Anonymous

                  thanks! Could you please let me know how to do this re-scoring? i am trying to find it in the tutorials but not successfull. thanks

                • September 23, 2019 at 6:42 pm #14987
                  Anonymous

                    I don’t remember, but off the top of my head, just run them all through score_jd2 with -in:file:native set to whichever model you want them compared to.  

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