[phenixbb] rosetta installation problem ubuntu 18.04
Billy Poon
BKPoon at lbl.gov
Mon Aug 20 10:03:18 PDT 2018
Hi Georg,
We've updated the Rosetta installation documentation for Rosetta 3.9. It
can be found at
https://www.phenix-online.org/version_docs/1.14-3235/reference/rosetta_install.html.
There is a note for Ubuntu 16.04 and greater because of a change in ABI for
GCC. Basically, a flag needs to be added during compilation so that Rosetta
libraries built with GCC >= 5.1 can be linked with the Phenix libraries
built with GCC 4.4.7 (CentOS 6). We provide the file, site.settings (
https://www.phenix-online.org/version_docs/1.14-3235/extras/site.settings),
and the location to put that
file, ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings.
One specific note for you is that when you add PHENIX_ROSETTA_PATH to your
.bashrc file, that variable is not set unless you open a new terminal. To
set in it the current shell, just run the "export
PHENIX_ROSETTA_PATH=/home/g/programs/rosetta_src_2016.32.58837_bundle/"
command in the shell.
To complete your installation, you can
1) Download and extract Rosetta 3.9
2) Run "export PHENIX_ROSETTA_PATH=/home/g/programs/<Rosetta 3.9 name>"
3) copy the site.settings file (
https://www.phenix-online.org/version_docs/1.14-3235/extras/site.settings)
to ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings
4) source <phenix installation directory>/phenix_env.sh
5) rosetta.build_phenix_interface nproc=8
6) rosetta.run_tests
Step 6 should finish without error.
Let us know of any other questions. Thanks!
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Sun, Aug 19, 2018 at 1:09 PM Georg Mlynek <georg.mlynek at univie.ac.at>
wrote:
> Dear Scientific Community, I am struggling installing rosetta on ubuntu
> 18.04.1 LTS and phenix 1.14-3211-000.
>
> I followed the instruction as in
>
> https://www.phenix-online.org/documentation/reference/rosetta_install.html
>
> the provided link
> https://c4c.uwc4c.com/express_license_technologies/rosetta
>
> gives an "This site can't be reached error"
>
> Therfore I went to https://www.rosettacommons.org/software
>
> and downloaded
>
> and unpacked in /home/g/programs/rosetta_src_2016.32.58837_bundle/
>
> I added the line
>
> export
> PHENIX_ROSETTA_PATH=/home/g/programs/rosetta_src_2016.32.58837_bundle/
>
> to .bashrc
>
> running
>
> rosetta.build_phenix_interface nproc=8
>
> I can't remember if it was fine. Running it now gives
>
> g at glap:~$ rosetta.build_phenix_interface nproc=8
> Substituting phenix.python into build shell scripts
> update_options.sh
> update_ResidueType_enum_files.sh
> Applying patch
> patching file source/src/core/kinematics/tree/Atom.hh
> Reversed (or previously applied) patch detected! Assume -R? [n]
>
> *pressing n*
>
> Apply anyway? [n] n
> Skipping patch.
> 2 out of 2 hunks ignored -- saving rejects to file
> source/src/core/kinematics/tree/Atom.hh.rej
> patching file source/src/core/kinematics/tree/Atom_.cc
> Hunk #1 FAILED at 817.
> 1 out of 1 hunk FAILED -- saving rejects to file
> source/src/core/kinematics/tree/Atom_.cc.rej
> patching file source/src/core/kinematics/tree/Atom_.hh
> Hunk #1 FAILED at 467.
> 1 out of 1 hunk FAILED -- saving rejects to file
> source/src/core/kinematics/tree/Atom_.hh.rej
> patching file source/src/core/kinematics/tree/BondedAtom.cc
> Hunk #1 FAILED at 542.
> 1 out of 1 hunk FAILED -- saving rejects to file
> source/src/core/kinematics/tree/BondedAtom.cc.rej
> patching file source/src/core/kinematics/tree/BondedAtom.hh
> Hunk #1 FAILED at 259.
> 1 out of 1 hunk FAILED -- saving rejects to file
> source/src/core/kinematics/tree/BondedAtom.hh.rej
> patch unexpectedly ends in middle of line
>
> Phenix modules found : /usr/local/phenix-1.14-3211/modules/phenix
> Traceback (most recent call last):
> File
> "/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py",
> line 265, in <module>
> run(sys.argv[1:])
> File
> "/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py",
> line 225, in run
> f=file("dispatcher_include_erraser.sh", "wb")
> IOError: [Errno 13] Permission denied: 'dispatcher_include_erraser.sh'
>
> *running the run test gives following.*
>
> lap:~$ rosetta.run_tests
> Running Rosetta refinement tests
>
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.pdb
>
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz
> phenix.rosetta_refine
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.pdb
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz
> number_of_models=2
>
> ============================== Collecting inputs
> ==============================
>
>
> ----------Processing X-ray
> data----------
>
> F-obs:
>
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
> Miller array info:
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
> Observation type: xray.amplitude
> Type of data: double, size=495
> Type of sigmas: double, size=495
> Number of Miller indices: 495
> Anomalous flag: False
> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
> Space group: P 1 21 1 (No. 4)
> Systematic absences: 0
> Centric reflections: 199
> Resolution range: 22.4416 1.80066
> Completeness in resolution range: 0.895118
> Completeness with d_max=infinity: 0.895118
> Wavelength: 1.0000
>
> Number of F-obs in resolution range: 495
> Number of F-obs<0 (these reflections will be rejected): 0
> Number of F-obs=0 (these reflections will be used in refinement): 0
> Refinement resolution range: d_max = 22.4416
> d_min = 1.8007
>
> R-free flags:
>
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
> Miller array info:
> /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
> Observation type: None
> Type of data: int, size=495
> Type of sigmas: None
> Number of Miller indices: 495
> Anomalous flag: False
> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
> Space group: P 1 21 1 (No. 4)
> Systematic absences: 0
> Centric reflections: 199
> Resolution range: 22.4416 1.80066
> Completeness in resolution range: 0.895118
> Completeness with d_max=infinity: 0.895118
> Wavelength: 1.0000
>
> Test (R-free flags) flag value: 1
>
> Number of work/free reflections by resolution:
> work free %free
> bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%
> bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%
> bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%
> bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%
> bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%
> bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%
> bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%
> bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%
> bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%
> bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%
> overall 475 20 4.0%
>
> ----------Processing PDB
> file(s)----------
>
> Monomer Library directory:
> "/usr/local/phenix-1.14-3211/modules/chem_data/mon_lib"
> Total number of atoms: 66
> Number of models: 1
> Model: ""
> Number of chains: 2
> Chain: "A"
> Number of atoms: 59
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 7, 59
> Classifications: {'peptide': 7}
> Modifications used: {'COO': 1}
> Link IDs: {'TRANS': 6}
> Chain: " "
> Number of atoms: 7
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 7, 7
> Classifications: {'water': 7}
> Link IDs: {None: 6}
> Time building chain proxies: 0.13, per 1000 atoms: 1.97
> Number of scatterers: 66
> At special positions: 0
> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
> Space group: P 1 21 1 (No. 4)
> Number of sites at special positions: 0
> Number of scattering types: 3
> Type Number sf(0)
> O 21 8.00
> N 12 7.00
> C 33 6.00
> sf(0) = scattering factor at diffraction angle 0.
>
> Number of disulfides: simple=0, symmetry=0
> Custom bonds:
> Warning: Ignoring bond with distance_ideal = None:
> atom_selection_1 = None
> atom_selection_2 = None
> Total number of custom bonds: 0
> Custom angles:
> Warning: Ignoring angle with angle_ideal = None:
> atom_selection_1 = None
> atom_selection_2 = None
> atom_selection_3 = None
> Total number of custom angles: 0
> Custom dihedrals:
> Warning: Ignoring dihedral with angle_ideal = None:
> atom_selection_1 = None
> atom_selection_2 = None
> atom_selection_3 = None
> atom_selection_4 = None
> Total number of custom dihedrals: 0
> Custom planarities:
> Warning: Ignoring planarity with with sigma <= 0:
> atom_selection = None
> None
> Total number of custom planarities: 0
> Custom parallelities:
> Warning: Ignoring parallelity with empty atom selection.
> Total number of custom parallelities: 0
>
> Automatic linking
> Parameters for automatic linking
> Linking & cutoffs
> Metal : False - 3.50
> Amimo acid : False - 1.90
> Carbohydrate : True - 1.99
> Ligands : True - 1.99
> Small molecules : False - 1.98
> Amino acid - RNA/DNA : False
>
> Number of custom bonds: simple=0, symmetry=0
> Time building additional restraints: 0.02
> Conformation dependent library (CDL) restraints added in 3.5 milliseconds
>
> Adding C-beta torsion restraints...
> Number of C-beta restraints generated: 12
>
> Time building geometry restraints manager: 0.02 seconds
>
> NOTE: a complete listing of the restraints can be obtained by requesting
> output of .geo file.
>
> Histogram of bond lengths:
> 1.23 - 1.29: 13
> 1.29 - 1.36: 11
> 1.36 - 1.42: 7
> 1.42 - 1.49: 6
> 1.49 - 1.55: 22
> Bond restraints: 59
> Sorted by residual:
> bond pdb=" N GLY A 1 "
> pdb=" CA GLY A 1 "
> ideal model delta sigma weight residual
> 1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01
> bond pdb=" CA GLN A 4 "
> pdb=" C GLN A 4 "
> ideal model delta sigma weight residual
> 1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00
> bond pdb=" N GLN A 4 "
> pdb=" CA GLN A 4 "
> ideal model delta sigma weight residual
> 1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00
> bond pdb=" CA ASN A 2 "
> pdb=" C ASN A 2 "
> ideal model delta sigma weight residual
> 1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00
> bond pdb=" CA ASN A 6 "
> pdb=" C ASN A 6 "
> ideal model delta sigma weight residual
> 1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00
> ... (remaining 54 not shown)
>
> Histogram of bond angle deviations from ideal:
> 107.05 - 110.59: 8
> 110.59 - 114.13: 19
> 114.13 - 117.67: 11
> 117.67 - 121.21: 23
> 121.21 - 124.75: 18
> Bond angle restraints: 79
> Sorted by residual:
> angle pdb=" N ASN A 3 "
> pdb=" CA ASN A 3 "
> pdb=" C ASN A 3 "
> ideal model delta sigma weight residual
> 108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00
> angle pdb=" N GLN A 4 "
> pdb=" CA GLN A 4 "
> pdb=" C GLN A 4 "
> ideal model delta sigma weight residual
> 108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00
> angle pdb=" CA GLN A 4 "
> pdb=" C GLN A 4 "
> pdb=" O GLN A 4 "
> ideal model delta sigma weight residual
> 120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00
> angle pdb=" CA GLN A 5 "
> pdb=" C GLN A 5 "
> pdb=" O GLN A 5 "
> ideal model delta sigma weight residual
> 120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00
> angle pdb=" C GLN A 4 "
> pdb=" N GLN A 5 "
> pdb=" CA GLN A 5 "
> ideal model delta sigma weight residual
> 123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00
> ... (remaining 74 not shown)
>
> Histogram of dihedral angle deviations from ideal:
> 0.04 - 14.51: 26
> 14.51 - 28.98: 5
> 28.98 - 43.45: 1
> 43.45 - 57.92: 1
> 57.92 - 72.39: 1
> Dihedral angle restraints: 34
> sinusoidal: 15
> harmonic: 19
> Sorted by residual:
> dihedral pdb=" CA ASN A 3 "
> pdb=" C ASN A 3 "
> pdb=" N GLN A 4 "
> pdb=" CA GLN A 4 "
> ideal model delta harmonic sigma weight residual
> 180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00
> dihedral pdb=" CB GLN A 5 "
> pdb=" CG GLN A 5 "
> pdb=" CD GLN A 5 "
> pdb=" OE1 GLN A 5 "
> ideal model delta sinusoidal sigma weight residual
> 0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00
> dihedral pdb=" CB GLN A 4 "
> pdb=" CG GLN A 4 "
> pdb=" CD GLN A 4 "
> pdb=" OE1 GLN A 4 "
> ideal model delta sinusoidal sigma weight residual
> 0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00
> ... (remaining 31 not shown)
>
> Histogram of chiral volume deviations from ideal:
> 0.000 - 0.024: 1
> 0.024 - 0.047: 1
> 0.047 - 0.071: 1
> 0.071 - 0.094: 1
> 0.094 - 0.118: 2
> Chirality restraints: 6
> Sorted by residual:
> chirality pdb=" CA GLN A 5 "
> pdb=" N GLN A 5 "
> pdb=" C GLN A 5 "
> pdb=" CB GLN A 5 "
> both_signs ideal model delta sigma weight residual
> False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01
> chirality pdb=" CA ASN A 6 "
> pdb=" N ASN A 6 "
> pdb=" C ASN A 6 "
> pdb=" CB ASN A 6 "
> both_signs ideal model delta sigma weight residual
> False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01
> chirality pdb=" CA ASN A 2 "
> pdb=" N ASN A 2 "
> pdb=" C ASN A 2 "
> pdb=" CB ASN A 2 "
> both_signs ideal model delta sigma weight residual
> False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01
> ... (remaining 3 not shown)
>
> Planarity restraints: 13
> Sorted by residual:
> delta sigma weight rms_deltas
> residual
> plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03
> 1.87e+00
> pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03
> pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03
> pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03
> pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03
> pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03
> pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03
> pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03
> delta sigma weight rms_deltas
> residual
> plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02
> 1.42e+00
> pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03
> pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03
> pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03
> delta sigma weight rms_deltas
> residual
> plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02
> 1.18e+00
> pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03
> pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03
> pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03
> ... (remaining 10 not shown)
>
> Histogram of nonbonded interaction distances:
> 2.53 - 3.00: 50
> 3.00 - 3.48: 107
> 3.48 - 3.95: 243
> 3.95 - 4.42: 255
> 4.42 - 4.90: 523
> Nonbonded interactions: 1178
> Sorted by model distance:
> nonbonded pdb=" OH TYR A 7 "
> pdb=" O HOH 11 "
> model vdw sym.op.
> 2.525 2.440 -x+1,y-1/2,-z+1
> nonbonded pdb=" O HOH 11 "
> pdb=" OH TYR A 7 "
> model vdw sym.op.
> 2.525 2.440 -x+1,y+1/2,-z+1
> nonbonded pdb=" O HOH 14 "
> pdb=" O HOH 13 "
> model vdw sym.op.
> 2.634 2.440 x,y-1,z
> nonbonded pdb=" O HOH 13 "
> pdb=" O HOH 14 "
> model vdw sym.op.
> 2.634 2.440 x,y+1,z
> nonbonded pdb=" N GLY A 1 "
> pdb=" O GLY A 1 "
> model vdw
> 2.665 2.496
> ... (remaining 1173 not shown)
>
> NOTE: a complete listing of the restraints can be obtained by requesting
> output of .geo file.
>
> ============================== Scattering factors
> =============================
>
>
> ----------X-ray scattering
> dictionary----------
>
> Number of scattering types: 3
> Type Number sf(0) Gaussians
> O 21 7.97 2
> N 12 6.97 2
> C 33 5.97 2
> sf(0) = scattering factor at diffraction angle 0.
>
> Number of scatterers: 66
> At special positions: 0
> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
> Space group: P 1 21 1 (No. 4)
>
> ----------F(model)
> initialization----------
>
> Twinning will be detected automatically.
> start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.:
> 495
> re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.:
> 495
> remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.:
> 493
> bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.:
> 493
> remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.:
> 493
> |--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 %
> free)--------------|
> |
> |
> | r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate):
> -0.00 A|
> |
> |
> | normalized target function (ml) (work):
> 2.637727 |
> | target function (ml) not normalized (work):
> 1247.644901 |
> | target function (ml) not normalized (free):
> 60.766973 |
>
> |-----------------------------------------------------------------------------|
>
> End of input processing
> Sorry:
> The RosettaScripts executable could not be located. Please set the
> environmental variable PHENIX_ROSETTA_PATH or add the appropriate
> directory to your PATH environment variable.
>
> *I am grateful for any advice.*
>
> *Best regards, Georg.*
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
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