how do you test if your rosetta.xxx is indeed correctly built?

Member Site Forums Rosetta++ Rosetta++ – General how do you test if your rosetta.xxx is indeed correctly built?

  • This topic has 4 replies, 2 voices, and was last updated 16 years ago by Anonymous.
Viewing 4 reply threads
  • Author
    Posts
    • #549
      Anonymous

        beginner question…

        what do you do to assess the quality of the generated executable?
        (there is no “make check” or “make test”)
        Is there some basic tests to run?

        Thanks,

        Tru

      • #3934
        Anonymous

          If you have a rosetta.xxx successfully generated, you can run a simple test with “-s xxx.pdb -design -fixbb -natrot” to get native structure energy information

          > beginner question…
          >
          > what do you do to assess the quality of the generated executable?
          > (there is no “make check” or “make test”)
          > Is there some basic tests to run?
          >
          > Thanks,
          >
          > Tru

        • #3938
          Anonymous

            > If you have a rosetta.xxx successfully generated, you can run a simple test with “-s xxx.pdb -design -fixbb -natrot” to get native structure energy information

            [tru@sillage samplerun]$ pwd
            /rosetta_documentation/docking/tutorial/examples/samplerun

            [tru@sillage samplerun]$ ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
            command executed: ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
            [T/F OPT]Default FALSE value for [-no_option_display]
            [T/F OPT]Default FALSE value for [-args_file]
            [STR OPT]Default value for [-paths] paths.txt.
            [T/F OPT]Default FALSE value for [-version]
            [T/F OPT]Default FALSE value for [-score]
            [T/F OPT]Default FALSE value for [-abinitio]
            [T/F OPT]Default FALSE value for [-refine]
            [T/F OPT]Default FALSE value for [-assemble]
            [T/F OPT]Default FALSE value for [-idealize]
            [T/F OPT]Default FALSE value for [-relax]
            [T/F OPT]Default FALSE value for [-abrelax]
            [T/F OPT]Default FALSE value for [-abrelax_mode]
            [T/F OPT]New TRUE value for [-design]
            [T/F OPT]Default FALSE value for [-onlypack]
            [T/F OPT]New TRUE value for [-fixbb]
            [T/F OPT]Default FALSE value for [-pack_in_parallel]
            [T/F OPT]Default FALSE value for [-directed_design]
            [REAL OPT]Default value for [-interface_electrostatic_complementarity_shift] 0
            [T/F OPT]Default FALSE value for [-reverse_comp]
            [INT OPT]Default value for [-conv_limit_mod] 3
            [STR OPT]Default value for [-chain_in_preferred_state] none.
            [STR OPT]Default value for [-chain_in_ref_state] none.
            [T/F OPT]Default FALSE value for [-rotamerize]
            [T/F OPT]Default FALSE value for [-point_mutation]
            [T/F OPT]Default FALSE value for [-mcmin_trials]
            [T/F OPT]Default FALSE value for [-output_design_movie]
            [T/F OPT]Default FALSE value for [-no_new_CG]
            [T/F OPT]Default FALSE value for [-multistate]
            [T/F OPT]Default FALSE value for [-dna_motifs]
            [REAL OPT]Default value for [-motifs_close_enough] 1.20000005
            [REAL OPT]Default value for [-motifs_far_dist] 5
            [REAL OPT]Default value for [-Motifs_bump_value] 100
            [REAL OPT]Default value for [-motifs_match_weight] 1
            [INT OPT]Default value for [-motifs_rots_required] 2
            ….
            [REAL OPT]Default value for [-mod_hhrep_height] 1
            [REAL OPT]Default value for [-mod_hhrep_width] 1
            [REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
            [REAL OPT]Default value for [-mod_hhrep_exponent] 4
            [REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
            [REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
            [STR OPT]New value for [-s] test.pdb.
            Starting structure: test
            Reading ../../../../../rosetta_database/Rama_smooth_dyn.dat_ss_6.4
            Reading ../../../../../rosetta_database/phi.theta.36.HS.resmooth
            Reading ../../../../../rosetta_database/phi.theta.36.SS.resmooth
            [STR OPT]Default value for [-atom_vdw_set] default.
            [T/F OPT]Default FALSE value for [-IUPAC]
            Atom_mode set to all
            [STR OPT]Default value for [-paircutoffs] paircutoffs.
            Reading ../../../../../rosetta_database/paircutoffs
            [T/F OPT]Default FALSE value for [-interface_ds]
            [T/F OPT]Default FALSE value for [-decoystats]
            set_decoystats_flag: from,to F F
            [T/F OPT]Default FALSE value for [-decoyfeatures]
            [T/F OPT]Default FALSE value for [-t32s3]
            [T/F OPT]Default FALSE value for [-evolution]
            [T/F OPT]Default FALSE value for [-evol_recomb]
            [T/F OPT]Default FALSE value for [-profile]
            [T/F OPT]Default FALSE value for [-dummy_model]
            [T/F OPT]Default FALSE value for [-saxs_model]
            Profile defined from q = 0 to 1.
            ERROR:: Can’t find starting structure: ../prepack/test.pdb
            ERROR:: Exit from: input_pdb.cc line: 3028

            -> *** Can’t find starting structure: ../prepack/test.pdb ***
            I guess I need another command to generate the “prepacked” pdb ;)

            Tru

          • #3941
            Anonymous

              It should be the path problem which specified in your path.txt. You might have the “prepacked” directory in your path file but it is not exist on your computer.

              > beginner question…
              >
              > what do you do to assess the quality of the generated executable?
              > (there is no “make check” or “make test”)
              > Is there some basic tests to run?
              >
              > Thanks,
              >
              > Tru

            • #3946
              Anonymous

                > It should be the path problem which specified in your path.txt. You might have the “prepacked” directory in your path file but it is not exist on your computer.

                I completely agree to your conclusion, but **how** is the prepacked directory
                generated ? I haven’t found any informations about it.

                Thanks

            Viewing 4 reply threads
            • You must be logged in to reply to this topic.