install rosetta problems

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    • May 13, 2011 at 1:44 am #910
      Anonymous

        Hi,
        I am trying install rosetta on the fedora system,with gcc 4.1.2 and scons 2.0.1. But I encountered a problem while I install with the command:scons bin mode=release.
        there are two warnings that always repeat again and again, I do not know how to solve this problem.
        scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
        File “/xtal_programs/rosetta3.2.1/rosetta_source/SConscript”, line 40, in

        scons: warning: No hashlib or MD5 module available, CacheDir() not supported
        File “/xtal_programs/AutoDock/mgltools-1.5.4/bin/scons-2.0.1”, line 190, in

        however, it seems that can still finish install rosetta. But Roseta does not work well whem I use phenix.mr_rosetta to solve a difficult structure that failed with phaser.
        Pls help
        Thanks
        C.Yan

      • May 13, 2011 at 3:59 am #5574
        Anonymous

          As a general rule, warnings are not problematic.

          Also, Rosetta has an included copy of SCons – you can try building with it to see if you like the results better.

          If the Rosetta install completes, and the MR executeable exists, then I don’t think recompiling is going to change the results. I don’t know enough about MR/phenix to suggest ways to improve it. What about the results makes you unhappy?

        • May 15, 2011 at 4:51 am #5578
          Anonymous

            At last, the program give the following message:
            ******************* ERROR ENDING ***************
            mr_rosetta failed…
            child process stderr output:
            command: ‘sh /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1’
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/rave:/xtal_programs/USF/sbin:/xtal_programs/USF/spasm:/xtal_programs/USF/voidoo:/xtal_programs/USF/xutil:/xtal_programs/O:/xtal_programs/O/data/omac:/xtal_programs/clustalw-2.1:/xtal_programs/multalin:/xtal_programs/ESPript-2_3-www-3_05/bin:/xtal_programs/shelx/linux:/xtal_programs/graphviz-2.20.2/bin:/xtal_programs/fasta-35.3.5:/xtal_programs/molscript-2.1.2:/xtal_programs/bobscript/bin:/xtal_programs/XDS:/xtal_programs/HKL2000:/xtal_programs/pseudo/bin:/xtal_programs/OASIS-2004/bin:/xtal_programs/sapipro:/xtal_programs/ha_ncs:/xtal_programs/snb2.2p1/bin:/xtal_programs/dssp:/xtal_programs/hole2/exe:/xtal_programs/automar:/xtal_programs/whatcheck:/xtal_programs/yasara:/xtal_programs/MoProSuite/bin-Linux:/xtal_programs/MoProSuite:/xtal_programs/atsas-2.4.0-1/bin:/xtal_programs/Situs_2.5/bin:/xtal_programs/vmd-1.9beta2:/xtal_programs/3D_Dock/progs:/xtal_programs/3D_Dock/multidock:/xtal_programs/REPLACE/bin/Linux:/xtal_programs/MIFit:/xtal_programs/Raster3D_2.7s:/xtal_programs/chimera/bin:/xtal_programs/untangle-0.7:/xtal_programs/xdsme-0.4.5/bin/noarch:/xtal_programs/solve-2.13/bin:/xtal_programs/USF/dejavu:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/rave:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/sbin:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/spasm:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/voidoo:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/xutil:/xtal_programs/O:: No such file or directory
            /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.sh: line 4: :/xtal_programs/O/data/omac:/xtal_programs/clustalw-2.1:/xtal_programs/multalin:/xtal_programs/ESPript-2_3-www-3_05/bin:/xtal_programs/shelx/linux:/xtal_programs/graphviz-2.20.2/bin:/xtal_programs/fasta-35.3.5:/xtal_programs/molscript-2.1.2:/xtal_programs/bobscript/bin:/xtal_programs/XDS:/xtal_programs/HKL2000:/xtal_programs/pseudo/bin:/xtal_programs/OASIS-2004/bin:/xtal_programs/sapipro:/xtal_programs/ha_ncs:/xtal_programs/snb2.2p1/bin:/xtal_programs/dssp:/xtal_programs/hole2/exe:/xtal_programs/automar:/xtal_programs/whatcheck:/xtal_programs/yasara:/xtal_programs/MoProSuite/bin-Linux:/xtal_programs/MoProSuite:/xtal_programs/atsas-2.4.0-1/bin:/xtal_programs/Situs_2.5/bin:/xtal_programs/vmd-1.9beta2:/xtal_programs/3D_Dock/progs:/xtal_programs/3D_Dock/multidock:/xtal_programs/REPLACE/bin/Linux:/xtal_programs/MIFit:/xtal_programs/Raster3D_2.7s:/xtal_programs/chimera/bin:/xtal_programs/untangle-0.7:/xtal_programs/xdsme-0.4.5/bin/noarch: No such file or directory

            ******************* ERROR ENDING ***************

          • May 16, 2011 at 1:06 am #5583
            Anonymous

              I install Rosetta at /xtal_programs/rosetta3.2.1/, and the contents of /rosetta_source/bin are:
              AbinitioRelax.default.linuxgccrelease
              AbinitioRelax.linuxgccrelease
              backrub.default.linuxgccrelease
              backrub.linuxgccrelease
              benchmark.default.linuxgccrelease
              benchmark.linuxgccrelease
              ca_to_allatom.default.linuxgccrelease
              ca_to_allatom.linuxgccrelease
              cluster_alns.default.linuxgccrelease
              cluster_alns.linuxgccrelease
              cluster.default.linuxgccrelease
              cluster.linuxgccrelease
              combine_silent.default.linuxgccrelease
              combine_silent.linuxgccrelease
              CstfileToTheozymePDB.default.linuxgccrelease
              CstfileToTheozymePDB.linuxgccrelease
              ddg_benchmark.default.linuxgccrelease
              ddg_benchmark.linuxgccrelease
              design_contrast_and_statistic.default.linuxgccrelease
              design_contrast_and_statistic.linuxgccrelease
              docking_prepack_protocol.default.linuxgccrelease
              docking_prepack_protocol.linuxgccrelease
              docking_protocol.default.linuxgccrelease
              docking_protocol.linuxgccrelease
              enzyme_design.default.linuxgccrelease
              enzyme_design.linuxgccrelease
              extract_atomtree_diffs.default.linuxgccrelease
              extract_atomtree_diffs.linuxgccrelease
              extract_pdbs.default.linuxgccrelease
              extract_pdbs.linuxgccrelease
              fixbb.default.linuxgccrelease
              fixbb.linuxgccrelease
              FlexPepDocking.default.linuxgccrelease
              FlexPepDocking.linuxgccrelease
              FloppyTail.default.linuxgccrelease
              FloppyTail.linuxgccrelease
              full_length_model.default.linuxgccrelease
              full_length_model.linuxgccrelease
              gen_apo_grids.default.linuxgccrelease
              gen_apo_grids.linuxgccrelease
              gen_lig_grids.default.linuxgccrelease
              gen_lig_grids.linuxgccrelease
              idealize.default.linuxgccrelease
              idealize_jd2.default.linuxgccrelease
              idealize_jd2.linuxgccrelease
              idealize.linuxgccrelease
              ligand_dock.default.linuxgccrelease
              ligand_dock.linuxgccrelease
              ligand_rpkmin.default.linuxgccrelease
              ligand_rpkmin.linuxgccrelease
              loopmodel.default.linuxgccrelease
              loopmodel.linuxgccrelease
              loops_from_density.default.linuxgccrelease
              loops_from_density.linuxgccrelease
              match.default.linuxgccrelease
              match.linuxgccrelease
              membrane_abinitio2.default.linuxgccrelease
              membrane_abinitio2.linuxgccrelease
              minirosetta.default.linuxgccrelease
              minirosetta_graphics.default.linuxgccrelease
              minirosetta_graphics.linuxgccrelease
              minirosetta.linuxgccrelease
              mr_protocols.default.linuxgccrelease
              mr_protocols.linuxgccrelease
              relax.default.linuxgccrelease
              relax.linuxgccrelease
              revert_design_to_native.default.linuxgccrelease
              revert_design_to_native.linuxgccrelease
              rosettaDNA.default.linuxgccrelease
              rosettaDNA.linuxgccrelease
              rosetta_scripts.default.linuxgccrelease
              rosetta_scripts.linuxgccrelease
              rotamer_recovery.default.linuxgccrelease
              rotamer_recovery.linuxgccrelease
              score_aln.default.linuxgccrelease
              score_aln.linuxgccrelease
              score_jd2.default.linuxgccrelease
              score_jd2.linuxgccrelease
              sequence_tolerance.default.linuxgccrelease
              sequence_tolerance.linuxgccrelease
              super_aln.default.linuxgccrelease
              super_aln.linuxgccrelease
              SymDock.default.linuxgccrelease
              SymDock.linuxgccrelease

            • May 16, 2011 at 4:04 pm #5585
              Anonymous

                Here is some advice from Tom Terwilliger (who did the phenix integration):

                It’s hard to tell from the error
                message. The first thing to try is to run the mr_rosetta regression tests
                and see if they pass:

                phenix_regression.wizards.test_command_line_rosetta_quick_tests

                If they pass, then it is something specific to the case at hand and the
                inputs, if they fail, it is something in the installation…

              • November 21, 2011 at 1:02 am #6283
                Anonymous

                  I am able to install the following files in /rosetta_source/bin:
                  AbinitioRelax.default.linuxgccdebug
                  AbinitioRelax.default.linuxgccrelease
                  AbinitioRelax.linuxgccdebug
                  AbinitioRelax.linuxgccrelease
                  AnchoredDesign.default.linuxgccdebug
                  AnchoredDesign.default.linuxgccrelease
                  AnchoredDesign.linuxgccdebug
                  AnchoredDesign.linuxgccrelease
                  AnchoredPDBCreator.default.linuxgccdebug
                  AnchoredPDBCreator.default.linuxgccrelease
                  AnchoredPDBCreator.linuxgccdebug
                  AnchoredPDBCreator.linuxgccrelease
                  AnchorFinder.default.linuxgccdebug
                  AnchorFinder.default.linuxgccrelease
                  AnchorFinder.linuxgccdebug
                  AnchorFinder.linuxgccrelease
                  antibody_mode.default.linuxgccdebug
                  antibody_mode.default.linuxgccrelease
                  antibody_mode.linuxgccdebug
                  antibody_mode.linuxgccrelease
                  backrub.default.linuxgccdebug
                  backrub.default.linuxgccrelease
                  backrub.linuxgccdebug
                  backrub.linuxgccrelease
                  benchmark.default.linuxgccdebug
                  benchmark.default.linuxgccrelease
                  benchmark.linuxgccdebug
                  benchmark.linuxgccrelease
                  BuildPeptide.default.linuxgccdebug
                  BuildPeptide.default.linuxgccrelease
                  BuildPeptide.linuxgccdebug
                  BuildPeptide.linuxgccrelease
                  ca_to_allatom.default.linuxgccdebug
                  ca_to_allatom.default.linuxgccrelease
                  ca_to_allatom.linuxgccdebug
                  ca_to_allatom.linuxgccrelease
                  cluster_alns.default.linuxgccdebug
                  cluster_alns.default.linuxgccrelease
                  cluster_alns.linuxgccdebug
                  cluster_alns.linuxgccrelease
                  cluster.default.linuxgccdebug
                  cluster.default.linuxgccrelease
                  cluster.linuxgccdebug
                  cluster.linuxgccrelease
                  combine_silent.default.linuxgccdebug
                  combine_silent.default.linuxgccrelease
                  combine_silent.linuxgccdebug
                  combine_silent.linuxgccrelease
                  CstfileToTheozymePDB.default.linuxgccdebug
                  CstfileToTheozymePDB.default.linuxgccrelease
                  CstfileToTheozymePDB.linuxgccdebug
                  CstfileToTheozymePDB.linuxgccrelease
                  ddg_benchmark.default.linuxgccdebug
                  ddg_benchmark.default.linuxgccrelease
                  ddg_benchmark.linuxgccdebug
                  ddg_benchmark.linuxgccrelease
                  ddg_monomer.default.linuxgccdebug
                  ddg_monomer.default.linuxgccrelease
                  ddg_monomer.linuxgccdebug
                  ddg_monomer.linuxgccrelease
                  design_contrast_and_statistic.default.linuxgccdebug
                  design_contrast_and_statistic.default.linuxgccrelease
                  design_contrast_and_statistic.linuxgccdebug
                  design_contrast_and_statistic.linuxgccrelease
                  docking_prepack_protocol.default.linuxgccdebug
                  docking_prepack_protocol.default.linuxgccrelease
                  docking_prepack_protocol.linuxgccdebug
                  docking_prepack_protocol.linuxgccrelease
                  docking_protocol.default.linuxgccdebug
                  docking_protocol.default.linuxgccrelease
                  docking_protocol.linuxgccdebug
                  docking_protocol.linuxgccrelease
                  enzyme_design.default.linuxgccdebug
                  enzyme_design.default.linuxgccrelease
                  enzyme_design.linuxgccdebug
                  enzyme_design.linuxgccrelease
                  extract_atomtree_diffs.default.linuxgccdebug
                  extract_atomtree_diffs.default.linuxgccrelease
                  extract_atomtree_diffs.linuxgccdebug
                  extract_atomtree_diffs.linuxgccrelease
                  extract_pdbs.default.linuxgccdebug
                  extract_pdbs.default.linuxgccrelease
                  extract_pdbs.linuxgccdebug
                  extract_pdbs.linuxgccrelease
                  fix_alignment_to_match_pdb.default.linuxgccdebug
                  fix_alignment_to_match_pdb.default.linuxgccrelease
                  fix_alignment_to_match_pdb.linuxgccdebug
                  fix_alignment_to_match_pdb.linuxgccrelease
                  fixbb.default.linuxgccdebug
                  fixbb.default.linuxgccrelease
                  fixbb.linuxgccdebug
                  fixbb.linuxgccrelease
                  FlexPepDocking.default.linuxgccdebug
                  FlexPepDocking.default.linuxgccrelease
                  FlexPepDocking.linuxgccdebug
                  FlexPepDocking.linuxgccrelease
                  FloppyTail.default.linuxgccdebug
                  FloppyTail.default.linuxgccrelease
                  FloppyTail.linuxgccdebug
                  FloppyTail.linuxgccrelease
                  fragment_picker.default.linuxgccdebug
                  fragment_picker.default.linuxgccrelease
                  fragment_picker.linuxgccdebug
                  fragment_picker.linuxgccrelease
                  full_length_model.default.linuxgccdebug
                  full_length_model.default.linuxgccrelease
                  full_length_model.linuxgccdebug
                  full_length_model.linuxgccrelease
                  gen_apo_grids.default.linuxgccdebug
                  gen_apo_grids.default.linuxgccrelease
                  gen_apo_grids.linuxgccdebug
                  gen_apo_grids.linuxgccrelease
                  gen_lig_grids.default.linuxgccdebug
                  gen_lig_grids.default.linuxgccrelease
                  gen_lig_grids.linuxgccdebug
                  gen_lig_grids.linuxgccrelease
                  idealize_jd2.default.linuxgccdebug
                  idealize_jd2.default.linuxgccrelease
                  idealize_jd2.linuxgccdebug
                  idealize_jd2.linuxgccrelease
                  InterfaceAnalyzer.default.linuxgccdebug
                  InterfaceAnalyzer.default.linuxgccrelease
                  InterfaceAnalyzer.linuxgccdebug
                  InterfaceAnalyzer.linuxgccrelease
                  ligand_dock.default.linuxgccdebug
                  ligand_dock.default.linuxgccrelease
                  ligand_dock.linuxgccdebug
                  ligand_dock.linuxgccrelease
                  ligand_rpkmin.default.linuxgccdebug
                  ligand_rpkmin.default.linuxgccrelease
                  ligand_rpkmin.linuxgccdebug
                  ligand_rpkmin.linuxgccrelease
                  loopmodel.default.linuxgccdebug
                  loopmodel.default.linuxgccrelease
                  loopmodel.linuxgccdebug
                  loopmodel.linuxgccrelease
                  loops_from_density.default.linuxgccdebug
                  loops_from_density.default.linuxgccrelease
                  loops_from_density.linuxgccdebug
                  loops_from_density.linuxgccrelease
                  match.default.linuxgccdebug
                  match.default.linuxgccrelease
                  match.linuxgccdebug
                  match.linuxgccrelease
                  membrane_abinitio2.default.linuxgccdebug
                  membrane_abinitio2.default.linuxgccrelease
                  membrane_abinitio2.linuxgccdebug
                  membrane_abinitio2.linuxgccrelease
                  minimize_with_cst.default.linuxgccdebug
                  minimize_with_cst.default.linuxgccrelease
                  minimize_with_cst.linuxgccdebug
                  minimize_with_cst.linuxgccrelease
                  minirosetta.default.linuxgccdebug
                  minirosetta.default.linuxgccrelease
                  minirosetta_graphics.default.linuxgccdebug
                  minirosetta_graphics.default.linuxgccrelease
                  minirosetta_graphics.linuxgccdebug
                  minirosetta_graphics.linuxgccrelease
                  minirosetta.linuxgccdebug
                  minirosetta.linuxgccrelease
                  mpi_msd.default.linuxgccdebug
                  mpi_msd.default.linuxgccrelease
                  mpi_msd.linuxgccdebug
                  mpi_msd.linuxgccrelease
                  mr_protocols.default.linuxgccdebug
                  mr_protocols.default.linuxgccrelease
                  mr_protocols.linuxgccdebug
                  mr_protocols.linuxgccrelease
                  pepspec_anchor_dock.default.linuxgccdebug
                  pepspec_anchor_dock.default.linuxgccrelease
                  pepspec_anchor_dock.linuxgccdebug
                  pepspec_anchor_dock.linuxgccrelease
                  pepspec.default.linuxgccdebug
                  pepspec.default.linuxgccrelease
                  pepspec.linuxgccdebug
                  pepspec.linuxgccrelease
                  relax.default.linuxgccdebug
                  relax.default.linuxgccrelease
                  relax.linuxgccdebug
                  relax.linuxgccrelease
                  revert_design_to_native.default.linuxgccdebug
                  revert_design_to_native.default.linuxgccrelease
                  revert_design_to_native.linuxgccdebug
                  revert_design_to_native.linuxgccrelease
                  rna_database.default.linuxgccdebug
                  rna_database.default.linuxgccrelease
                  rna_database.linuxgccdebug
                  rna_database.linuxgccrelease
                  rna_denovo.default.linuxgccdebug
                  rna_denovo.default.linuxgccrelease
                  rna_denovo.linuxgccdebug
                  rna_denovo.linuxgccrelease
                  rna_design.default.linuxgccdebug
                  rna_design.default.linuxgccrelease
                  rna_design.linuxgccdebug
                  rna_design.linuxgccrelease
                  rna_extract.default.linuxgccdebug
                  rna_extract.default.linuxgccrelease
                  rna_extract.linuxgccdebug
                  rna_extract.linuxgccrelease
                  rosettaDNA.default.linuxgccdebug
                  rosettaDNA.default.linuxgccrelease
                  rosettaDNA.linuxgccdebug
                  rosettaDNA.linuxgccrelease
                  rosetta_scripts.default.linuxgccdebug
                  rosetta_scripts.default.linuxgccrelease
                  rosetta_scripts.linuxgccdebug
                  rosetta_scripts.linuxgccrelease
                  rotamer_recovery.default.linuxgccdebug
                  rotamer_recovery.default.linuxgccrelease
                  rotamer_recovery.linuxgccdebug
                  rotamer_recovery.linuxgccrelease
                  score_aln2.default.linuxgccdebug
                  score_aln2.default.linuxgccrelease
                  score_aln2.linuxgccdebug
                  score_aln2.linuxgccrelease
                  score_aln.default.linuxgccdebug
                  score_aln.default.linuxgccrelease
                  score_aln.linuxgccdebug
                  score_aln.linuxgccrelease
                  score.default.linuxgccdebug
                  score.default.linuxgccrelease
                  score_jd2.default.linuxgccdebug
                  score_jd2.default.linuxgccrelease
                  score_jd2.linuxgccdebug
                  score_jd2.linuxgccrelease
                  score.linuxgccdebug
                  score.linuxgccrelease
                  sequence_recovery.default.linuxgccdebug
                  sequence_recovery.default.linuxgccrelease
                  sequence_recovery.linuxgccdebug
                  sequence_recovery.linuxgccrelease
                  sequence_tolerance.default.linuxgccdebug
                  sequence_tolerance.default.linuxgccrelease
                  sequence_tolerance.linuxgccdebug
                  sequence_tolerance.linuxgccrelease
                  super_aln.default.linuxgccdebug
                  super_aln.default.linuxgccrelease
                  super_aln.linuxgccdebug
                  super_aln.linuxgccrelease
                  SymDock.default.linuxgccdebug
                  SymDock.default.linuxgccrelease
                  SymDock.linuxgccdebug
                  SymDock.linuxgccrelease
                  UBQ_E2_thioester.default.linuxgccdebug
                  UBQ_E2_thioester.default.linuxgccrelease
                  UBQ_E2_thioester.linuxgccdebug
                  UBQ_E2_thioester.linuxgccrelease
                  I want to know what is the next procedure to follow after this as I am not able to find and gcc file which I can use to make…can anyone please help to proceed further???

                • May 14, 2011 at 2:04 pm #5577
                  Anonymous

                    The molecular replacement runs as following:

                    Starting sub-processes Place model…
                    ==============================================================================

                    Splitting work into 1 jobs and running with 1 processors using sh
                    background=None in /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1

                    Starting job 1…Log will be: /raid/u6/Home/Ada/20110504/proc/HKL/structure/Rosetta/MR_ROSETTA_6/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

                    Then the molecular replacement is paused, I don’t know why

                  • May 15, 2011 at 7:35 pm #5582
                    Anonymous

                      This doesn’t look to me like it’s failing inside Rosetta, it looks like it’s having trouble finding a whole bunch of other programs (notice the repeated “No such file or directory” errors.) Do you know where the Rosetta installation is? If so, can you tell me the contents of the bin/ subfolder in the Rosetta directory (probably rosetta_source/bin?)

                    • November 21, 2011 at 9:46 pm #6290
                      Anonymous

                        Those are symlinks to your executables. You can run those files directly. I don’t understand what your question is – you’ve already used GCC (via scons) and don’t need make.

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