Rosetta3 Tutorials

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  • This topic has 8 replies, 5 voices, and was last updated 5 years ago by Anonymous.
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    • November 18, 2011 at 3:33 pm #2280
      Anonymous

        At RosettaCON2011, many of the developers and users got together to write documentation for an afternoon under the beautiful, central Washington sunshine. These tutorials will be officially released shortly (at the same download location as Rosetta, http://www.rosettacommons.org/software/).

        If you find errors in the documentation, please post them here and maybe they can get fixed. If you have suggestions for similar-depth tutorials not already covered, also post them here, and if we do it again in 2012 or 2013 they may go on the list.

      • November 21, 2011 at 12:41 am #6282
        Anonymous

          I am new to roseta and trying to install rosetta3.3_bundle on suse 11.3 machine. Can anyone help me to have step-by step installation guide as I am not an advanced use of linux OS.I am pretty not sure with the compilation and build process and bnit confused on those.

          Your help would be gratly appreciated!!!!!

        • December 17, 2012 at 9:50 am #8239
          Anonymous

            i am using rosetta 3.3 and encountered a problem. How can I fix that problem
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            ‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
            core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file /home/ammarah/Documents/LHB/LHB_09_05.200_v1_3
            core.io.fragments: reading fragments from file: /home/ammarah/Documents/LHB/LHB_03_05.200_v1_3 …
            core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
            core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/ammarah/Documents/LHB/LHB_03_05.200_v1_3
            core.fragment: compute strand/loop fractions for 389 residues…
            protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: phi.theta.36.HS.resmooth
            basic.io.database: Database file opened: phi.theta.36.SS.resmooth
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            protocols.jobdist.JobDistributors: S_00000896
            protocols.jobdist.JobDistributors: S_00000897
            protocols.jobdist.JobDistributors: S_00000898
            protocols.jobdist.JobDistributors: S_00000899
            protocols.jobdist.JobDistributors: S_00000900
            protocols.jobdist.JobDistributors: S_00000901
            protocols.jobdist.JobDistributors: S_00000902
            protocols.jobdist.JobDistributors: S_00000903
            protocols.jobdist.JobDistributors: S_00000904
            protocols.jobdist.JobDistributors: S_00000905
            protocols.jobdist.JobDistributors: S_00000906
            protocols.jobdist.JobDistributors: S_00000907
            protocols.jobdist.JobDistributors: S_00000908
            protocols.jobdist.JobDistributors: S_00000909
            protocols.jobdist.JobDistributors: S_00000910
            protocols.jobdist.JobDistributors: S_00000911
            protocols.jobdist.JobDistributors: S_00000912
            protocols.jobdist.JobDistributors: S_00000913
            protocols.jobdist.JobDistributors: S_00000914
            protocols.jobdist.JobDistributors: S_00000915
            protocols.jobdist.JobDistributors: S_00000916
            protocols.jobdist.JobDistributors: S_00000917
            protocols.jobdist.JobDistributors: S_00000918
            protocols.jobdist.JobDistributors: S_00000919
            protocols.jobdist.JobDistributors: S_00000920
            protocols.jobdist.JobDistributors: S_00000921
            protocols.jobdist.JobDistributors: S_00000922
            protocols.jobdist.JobDistributors: S_00000923
            protocols.jobdist.JobDistributors: S_00000924
            protocols.jobdist.JobDistributors: S_00000925
            protocols.jobdist.JobDistributors: S_00000926
            protocols.jobdist.JobDistributors: S_00000927
            protocols.jobdist.JobDistributors: S_00000928
            protocols.jobdist.JobDistributors: S_00000929
            protocols.jobdist.JobDistributors: S_00000930
            protocols.jobdist.JobDistributors: S_00000931
            protocols.jobdist.JobDistributors: S_00000932
            protocols.jobdist.JobDistributors: S_00000933
            protocols.jobdist.JobDistributors: S_00000934
            protocols.jobdist.JobDistributors: S_00000935
            protocols.jobdist.JobDistributors: S_00000936
            protocols.jobdist.JobDistributors: S_00000937
            protocols.jobdist.JobDistributors: S_00000938
            protocols.jobdist.JobDistributors: S_00000939
            protocols.jobdist.JobDistributors: S_00000940
            protocols.jobdist.JobDistributors: S_00000941
            protocols.jobdist.JobDistributors: S_00000942
            protocols.jobdist.JobDistributors: S_00000943
            protocols.jobdist.JobDistributors: S_00000944
            protocols.jobdist.JobDistributors: S_00000945
            protocols.jobdist.JobDistributors: S_00000946
            protocols.jobdist.JobDistributors: S_00000947
            protocols.jobdist.JobDistributors: S_00000948
            protocols.jobdist.JobDistributors: S_00000949
            protocols.jobdist.JobDistributors: S_00000950
            protocols.jobdist.JobDistributors: S_00000951
            protocols.jobdist.JobDistributors: S_00000952
            protocols.jobdist.JobDistributors: S_00000953
            protocols.jobdist.JobDistributors: S_00000954
            protocols.jobdist.JobDistributors: S_00000955
            protocols.jobdist.JobDistributors: S_00000956
            protocols.jobdist.JobDistributors: S_00000957
            protocols.jobdist.JobDistributors: S_00000958
            protocols.jobdist.JobDistributors: S_00000959
            protocols.jobdist.JobDistributors: S_00000960
            protocols.jobdist.JobDistributors: S_00000961
            protocols.jobdist.JobDistributors: S_00000962
            protocols.jobdist.JobDistributors: S_00000963
            protocols.jobdist.JobDistributors: S_00000964
            protocols.jobdist.JobDistributors: S_00000965
            protocols.jobdist.JobDistributors: S_00000966
            protocols.jobdist.JobDistributors: S_00000967
            protocols.jobdist.JobDistributors: S_00000968
            protocols.jobdist.JobDistributors: S_00000969
            protocols.jobdist.JobDistributors: S_00000970
            protocols.jobdist.JobDistributors: S_00000971
            protocols.jobdist.JobDistributors: S_00000972
            protocols.jobdist.JobDistributors: S_00000973
            protocols.jobdist.JobDistributors: S_00000974
            protocols.jobdist.JobDistributors: S_00000975
            protocols.jobdist.JobDistributors: S_00000976
            protocols.jobdist.JobDistributors: S_00000977
            protocols.jobdist.JobDistributors: S_00000978
            protocols.jobdist.JobDistributors: S_00000979
            protocols.jobdist.JobDistributors: S_00000980
            protocols.jobdist.JobDistributors: S_00000981
            protocols.jobdist.JobDistributors: S_00000982
            protocols.jobdist.JobDistributors: S_00000983
            protocols.jobdist.JobDistributors: S_00000984
            protocols.jobdist.JobDistributors: S_00000985
            protocols.jobdist.JobDistributors: S_00000986
            protocols.jobdist.JobDistributors: S_00000987
            protocols.jobdist.JobDistributors: S_00000988
            protocols.jobdist.JobDistributors: S_00000989
            protocols.jobdist.JobDistributors: S_00000990
            protocols.jobdist.JobDistributors: S_00000991
            protocols.jobdist.JobDistributors: S_00000992
            protocols.jobdist.JobDistributors: S_00000993
            protocols.jobdist.JobDistributors: S_00000994
            protocols.jobdist.JobDistributors: S_00000995
            protocols.jobdist.JobDistributors: S_00000996
            protocols.jobdist.JobDistributors: S_00000997
            protocols.jobdist.JobDistributors: S_00000998
            protocols.jobdist.JobDistributors: S_00000999
            protocols.jobdist.JobDistributors: S_00001000
            core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
            core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
            core.scoring.etable: Starting energy table calculation
            core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
            core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
            core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
            core.scoring.etable: Finished calculating energy tables.
            basic.io.database: Database file opened: pdb_pair_stats_fine
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: CEN6_mem_env_log.txt
            basic.io.database: Database file opened: CEN10_mem_env_log.txt
            basic.io.database: Database file opened: memcbeta_den.txt
            basic.io.database: Database file opened: mem_pair_log.txt
            basic.io.database: Database file opened: P_AA
            basic.io.database: Database file opened: P_AA_n
            basic.io.database: Database file opened: P_AA_pp
            basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
            protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
            protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
            protocols::checkpoint: Deleting checkpoints of Abrelax

          • June 14, 2019 at 7:36 am #14772
            Anonymous

              Hello,

              My pyrosetta do not have rosetta/bin or pyrosetta/bin. So I can not run match.linuxgccrelease and so on. why?

              Thanks for any help!

               

               

              • July 9, 2019 at 5:24 pm #14822
                Anonymous

                  PyRosetta is the Python interface to Rosetta. The intended use case for PyRosetta is to access it through Python, using custom written Python scripts. This is different from the standard command line Rosetta, which is accessed through the compiled applications such as match.linuxgccrelease.

                  If you want to use the compiled applications, I’d recommend using the regular (command line) Rosetta instead of PyRosetta. There should be no problem with downloading and installing both PyRosetta and Rosetta to the same computer, so you can switch between PyRosetta and commandline Rosetta as you please.

                  The other option is to take the protocol being run by the particular application and recapitulate it using the availible PyRosetta tools. For example, match.linuxgccrelease  uses protocols.match.Matcher, protocols.match.MatcherTask and protocols.match.MatchProcessor to do what it does. It would be possible (if a bit laborious) to re-create that within PyRosetta. — Though I’d only do that if downloading. installing and using the regular command line Rosetta was insufficient for your needs.

              • November 21, 2011 at 9:49 pm #6291
                Anonymous

                  We don’t offer “step by step building instructions” because invariably all users start with a different amount of knowledge, and 75% of the knowledge is different for different computers anyway. Here’s a vague outline:

                  1) download rosetta
                  2) untar rosetta
                  3) in the main rosetta directory, type “scons.py bin mode=release”
                  4) make sure it says “scons: done building targets”
                  5) if so, your executables are installed to folder bin in the rosetta directory and are ready to use.

                  Of course, there are 500 things that can go wrong, but those vary from machine to machine…

                • November 22, 2011 at 12:07 am #6293
                  Anonymous

                    I have long list of files in my rosetta/bin directory:/rosetta_source/bin> ls
                    AbinitioRelax.default.linuxgccdebug extract_atomtree_diffs.static.linuxgccrelease mpi_msd.static.linuxgccrelease
                    AbinitioRelax.default.linuxgccrelease extract_pdbs.default.linuxgccdebug mr_protocols.default.linuxgccdebug
                    AbinitioRelax.linuxgccdebug extract_pdbs.default.linuxgccrelease mr_protocols.default.linuxgccrelease
                    AbinitioRelax.linuxgccrelease extract_pdbs.linuxgccdebug mr_protocols.linuxgccdebug
                    AbinitioRelax.static.linuxgccdebug extract_pdbs.linuxgccrelease mr_protocols.linuxgccrelease
                    AbinitioRelax.static.linuxgccrelease extract_pdbs.static.linuxgccrelease mr_protocols.static.linuxgccrelease
                    AnchoredDesign.default.linuxgccdebug fix_alignment_to_match_pdb.default.linuxgccdebug pepspec_anchor_dock.default.linuxgccdebug
                    AnchoredDesign.default.linuxgccrelease fix_alignment_to_match_pdb.default.linuxgccrelease pepspec_anchor_dock.default.linuxgccrelease
                    AnchoredDesign.linuxgccdebug fix_alignment_to_match_pdb.linuxgccdebug pepspec_anchor_dock.linuxgccdebug
                    AnchoredDesign.linuxgccrelease fix_alignment_to_match_pdb.linuxgccrelease pepspec_anchor_dock.linuxgccrelease
                    AnchoredDesign.static.linuxgccdebug fix_alignment_to_match_pdb.static.linuxgccrelease pepspec_anchor_dock.static.linuxgccrelease
                    AnchoredDesign.static.linuxgccrelease fixbb.default.linuxgccdebug pepspec.default.linuxgccdebug
                    AnchoredPDBCreator.default.linuxgccdebug fixbb.default.linuxgccrelease pepspec.default.linuxgccrelease
                    AnchoredPDBCreator.default.linuxgccrelease fixbb.linuxgccdebug pepspec.linuxgccdebug
                    AnchoredPDBCreator.linuxgccdebug fixbb.linuxgccrelease pepspec.linuxgccrelease
                    AnchoredPDBCreator.linuxgccrelease fixbb.static.linuxgccrelease pepspec.static.linuxgccrelease
                    AnchoredPDBCreator.static.linuxgccdebug FlexPepDocking.default.linuxgccdebug relax.default.linuxgccdebug
                    AnchoredPDBCreator.static.linuxgccrelease FlexPepDocking.default.linuxgccrelease relax.default.linuxgccrelease
                    AnchorFinder.default.linuxgccdebug FlexPepDocking.linuxgccdebug relax.linuxgccdebug
                    AnchorFinder.default.linuxgccrelease FlexPepDocking.linuxgccrelease relax.linuxgccrelease
                    AnchorFinder.linuxgccdebug FlexPepDocking.static.linuxgccdebug relax.static.linuxgccrelease
                    AnchorFinder.linuxgccrelease FlexPepDocking.static.linuxgccrelease revert_design_to_native.default.linuxgccdebug
                    AnchorFinder.static.linuxgccdebug FloppyTail.default.linuxgccdebug revert_design_to_native.default.linuxgccrelease
                    AnchorFinder.static.linuxgccrelease FloppyTail.default.linuxgccrelease revert_design_to_native.linuxgccdebug
                    antibody_mode.default.linuxgccdebug FloppyTail.linuxgccdebug revert_design_to_native.linuxgccrelease
                    antibody_mode.default.linuxgccrelease FloppyTail.linuxgccrelease revert_design_to_native.static.linuxgccrelease
                    antibody_mode.linuxgccdebug FloppyTail.static.linuxgccdebug rna_database.default.linuxgccdebug
                    antibody_mode.linuxgccrelease FloppyTail.static.linuxgccrelease rna_database.default.linuxgccrelease
                    antibody_mode.static.linuxgccdebug fragment_picker.default.linuxgccdebug rna_database.linuxgccdebug
                    antibody_mode.static.linuxgccrelease fragment_picker.default.linuxgccrelease rna_database.linuxgccrelease
                    backrub.default.linuxgccdebug fragment_picker.linuxgccdebug rna_database.static.linuxgccrelease
                    backrub.default.linuxgccrelease fragment_picker.linuxgccrelease rna_denovo.default.linuxgccdebug
                    backrub.linuxgccdebug fragment_picker.static.linuxgccrelease rna_denovo.default.linuxgccrelease
                    backrub.linuxgccrelease full_length_model.default.linuxgccdebug rna_denovo.linuxgccdebug
                    backrub.static.linuxgccdebug full_length_model.default.linuxgccrelease rna_denovo.linuxgccrelease
                    backrub.static.linuxgccrelease full_length_model.linuxgccdebug rna_denovo.static.linuxgccrelease
                    benchmark.default.linuxgccdebug full_length_model.linuxgccrelease rna_design.default.linuxgccdebug
                    benchmark.default.linuxgccrelease full_length_model.static.linuxgccrelease rna_design.default.linuxgccrelease
                    benchmark.linuxgccdebug gen_apo_grids.default.linuxgccdebug rna_design.linuxgccdebug
                    benchmark.linuxgccrelease gen_apo_grids.default.linuxgccrelease rna_design.linuxgccrelease
                    benchmark.static.linuxgccdebug gen_apo_grids.linuxgccdebug rna_design.static.linuxgccrelease
                    benchmark.static.linuxgccrelease gen_apo_grids.linuxgccrelease rna_extract.default.linuxgccdebug
                    BuildPeptide.default.linuxgccdebug gen_apo_grids.static.linuxgccrelease rna_extract.default.linuxgccrelease
                    BuildPeptide.default.linuxgccrelease gen_lig_grids.default.linuxgccdebug rna_extract.linuxgccdebug
                    BuildPeptide.linuxgccdebug gen_lig_grids.default.linuxgccrelease rna_extract.linuxgccrelease
                    BuildPeptide.linuxgccrelease gen_lig_grids.linuxgccdebug rna_extract.static.linuxgccrelease
                    BuildPeptide.static.linuxgccdebug gen_lig_grids.linuxgccrelease rosettaDNA.default.linuxgccdebug
                    BuildPeptide.static.linuxgccrelease gen_lig_grids.static.linuxgccrelease rosettaDNA.default.linuxgccrelease
                    ca_to_allatom.default.linuxgccdebug idealize_jd2.default.linuxgccdebug rosettaDNA.linuxgccdebug
                    ca_to_allatom.default.linuxgccrelease idealize_jd2.default.linuxgccrelease rosettaDNA.linuxgccrelease
                    ca_to_allatom.linuxgccdebug idealize_jd2.linuxgccdebug rosettaDNA.static.linuxgccrelease
                    ca_to_allatom.linuxgccrelease idealize_jd2.linuxgccrelease rosetta_scripts.default.linuxgccdebug
                    ca_to_allatom.static.linuxgccrelease idealize_jd2.static.linuxgccrelease rosetta_scripts.default.linuxgccrelease
                    cluster_alns.default.linuxgccdebug InterfaceAnalyzer.default.linuxgccdebug rosetta_scripts.linuxgccdebug
                    cluster_alns.default.linuxgccrelease InterfaceAnalyzer.default.linuxgccrelease rosetta_scripts.linuxgccrelease
                    cluster_alns.linuxgccdebug InterfaceAnalyzer.linuxgccdebug rosetta_scripts.static.linuxgccrelease
                    cluster_alns.linuxgccrelease InterfaceAnalyzer.linuxgccrelease rotamer_recovery.default.linuxgccdebug
                    cluster_alns.static.linuxgccrelease InterfaceAnalyzer.static.linuxgccdebug rotamer_recovery.default.linuxgccrelease
                    cluster.default.linuxgccdebug InterfaceAnalyzer.static.linuxgccrelease rotamer_recovery.linuxgccdebug
                    cluster.default.linuxgccrelease ligand_dock.default.linuxgccdebug rotamer_recovery.linuxgccrelease
                    cluster.linuxgccdebug ligand_dock.default.linuxgccrelease rotamer_recovery.static.linuxgccrelease
                    cluster.linuxgccrelease ligand_dock.linuxgccdebug score_aln2.default.linuxgccdebug
                    cluster.static.linuxgccrelease ligand_dock.linuxgccrelease score_aln2.default.linuxgccrelease
                    combine_silent.default.linuxgccdebug ligand_dock.static.linuxgccrelease score_aln2.linuxgccdebug
                    combine_silent.default.linuxgccrelease ligand_rpkmin.default.linuxgccdebug score_aln2.linuxgccrelease
                    combine_silent.linuxgccdebug ligand_rpkmin.default.linuxgccrelease score_aln2.static.linuxgccrelease
                    combine_silent.linuxgccrelease ligand_rpkmin.linuxgccdebug score_aln.default.linuxgccdebug
                    combine_silent.static.linuxgccrelease ligand_rpkmin.linuxgccrelease score_aln.default.linuxgccrelease
                    CstfileToTheozymePDB.default.linuxgccdebug ligand_rpkmin.static.linuxgccrelease score_aln.linuxgccdebug
                    CstfileToTheozymePDB.default.linuxgccrelease loopmodel.default.linuxgccdebug score_aln.linuxgccrelease
                    CstfileToTheozymePDB.linuxgccdebug loopmodel.default.linuxgccrelease score_aln.static.linuxgccrelease
                    CstfileToTheozymePDB.linuxgccrelease loopmodel.linuxgccdebug score.default.linuxgccdebug
                    CstfileToTheozymePDB.static.linuxgccdebug loopmodel.linuxgccrelease score.default.linuxgccrelease
                    CstfileToTheozymePDB.static.linuxgccrelease loopmodel.static.linuxgccrelease score_jd2.default.linuxgccdebug
                    ddg_benchmark.default.linuxgccdebug loops_from_density.default.linuxgccdebug score_jd2.default.linuxgccrelease
                    ddg_benchmark.default.linuxgccrelease loops_from_density.default.linuxgccrelease score_jd2.linuxgccdebug
                    ddg_benchmark.linuxgccdebug loops_from_density.linuxgccdebug score_jd2.linuxgccrelease
                    ddg_benchmark.linuxgccrelease loops_from_density.linuxgccrelease score_jd2.static.linuxgccrelease
                    ddg_benchmark.static.linuxgccrelease loops_from_density.static.linuxgccrelease score.linuxgccdebug
                    ddg_monomer.default.linuxgccdebug match.default.linuxgccdebug score.linuxgccrelease
                    ddg_monomer.default.linuxgccrelease match.default.linuxgccrelease score.static.linuxgccrelease
                    ddg_monomer.linuxgccdebug match.linuxgccdebug sequence_recovery.default.linuxgccdebug
                    ddg_monomer.linuxgccrelease match.linuxgccrelease sequence_recovery.default.linuxgccrelease
                    ddg_monomer.static.linuxgccrelease match.static.linuxgccrelease sequence_recovery.linuxgccdebug
                    design_contrast_and_statistic.default.linuxgccdebug membrane_abinitio2.default.linuxgccdebug sequence_recovery.linuxgccrelease
                    design_contrast_and_statistic.default.linuxgccrelease membrane_abinitio2.default.linuxgccrelease sequence_recovery.static.linuxgccrelease
                    design_contrast_and_statistic.linuxgccdebug membrane_abinitio2.linuxgccdebug sequence_tolerance.default.linuxgccdebug
                    design_contrast_and_statistic.linuxgccrelease membrane_abinitio2.linuxgccrelease sequence_tolerance.default.linuxgccrelease
                    design_contrast_and_statistic.static.linuxgccrelease membrane_abinitio2.static.linuxgccrelease sequence_tolerance.linuxgccdebug
                    docking_prepack_protocol.default.linuxgccdebug minimize_with_cst.default.linuxgccdebug sequence_tolerance.linuxgccrelease
                    docking_prepack_protocol.default.linuxgccrelease minimize_with_cst.default.linuxgccrelease sequence_tolerance.static.linuxgccrelease
                    docking_prepack_protocol.linuxgccdebug minimize_with_cst.linuxgccdebug super_aln.default.linuxgccdebug
                    docking_prepack_protocol.linuxgccrelease minimize_with_cst.linuxgccrelease super_aln.default.linuxgccrelease
                    docking_prepack_protocol.static.linuxgccrelease minimize_with_cst.static.linuxgccrelease super_aln.linuxgccdebug
                    docking_protocol.default.linuxgccdebug minirosetta.default.linuxgccdebug super_aln.linuxgccrelease
                    docking_protocol.default.linuxgccrelease minirosetta.default.linuxgccrelease super_aln.static.linuxgccrelease
                    docking_protocol.linuxgccdebug minirosetta_graphics.default.linuxgccdebug SymDock.default.linuxgccdebug
                    docking_protocol.linuxgccrelease minirosetta_graphics.default.linuxgccrelease SymDock.default.linuxgccrelease
                    docking_protocol.static.linuxgccrelease minirosetta_graphics.linuxgccdebug SymDock.linuxgccdebug
                    enzyme_design.default.linuxgccdebug minirosetta_graphics.linuxgccrelease SymDock.linuxgccrelease
                    enzyme_design.default.linuxgccrelease minirosetta_graphics.static.linuxgccrelease SymDock.static.linuxgccdebug
                    enzyme_design.linuxgccdebug minirosetta.linuxgccdebug SymDock.static.linuxgccrelease
                    enzyme_design.linuxgccrelease minirosetta.linuxgccrelease UBQ_E2_thioester.default.linuxgccdebug
                    enzyme_design.static.linuxgccrelease minirosetta.static.linuxgccrelease UBQ_E2_thioester.default.linuxgccrelease
                    extract_atomtree_diffs.default.linuxgccdebug mpi_msd.default.linuxgccdebug UBQ_E2_thioester.linuxgccdebug
                    extract_atomtree_diffs.default.linuxgccrelease mpi_msd.default.linuxgccrelease UBQ_E2_thioester.linuxgccrelease
                    extract_atomtree_diffs.linuxgccdebug mpi_msd.linuxgccdebug UBQ_E2_thioester.static.linuxgccdebug
                    extract_atomtree_diffs.linuxgccrelease mpi_msd.linuxgccrelease UBQ_E2_thioester.static.linuxgccrelease

                    Do i need to compile them every time i use them for a program, Is my rosetta is finally ready to use??

                  • November 22, 2011 at 2:35 am #6294
                    Anonymous

                      Those are compiled. It appears to be ready to use. You do not need to recompile for each use, only if you make changes to the code (cc and hh files), get a new version of Rosetta, or move it to a different computer.

                    • December 17, 2012 at 2:57 pm #8240
                      Anonymous

                        Hi,

                        1) You should start your own thread,

                        2) It’s not clear to me from that log file that there is an error, but if there is one, it’s that your fragments file is messed up. Where did you get your fragments file from? The Robetta webserver?

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