install rosetta problems

[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

[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?

[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 ***************

[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

[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…

[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???

[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

[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?)

[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.

[Author]

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