Rosetta3 Tutorials

[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.

[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!!!!!

[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_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

[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!

 

 

[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.

[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…

[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??

[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.

[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?

[Author]

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