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rosetta for phenix directory cannot be found error

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rosetta for phenix directory cannot be found error
#1


Dear All,

Based on "https://www.phenix-online.org/documentation/reference/rosetta_install.html" I have installed the recent rosetta_src_2020.08.61146_bundle, and I have included "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/" in my .bashrc and have it sourced, with"/your-path-to-rosetta-here/" as the directory containing "demos   main    tools".

Because I have a recent version of GCC, I use the content in "https://www.phenix-online.org/documentation/extras/site.settings" as the site.settings.

However when I run "rosetta.run_tests", I meet the issue: OSError: [Errno 2] No such file or directory: '/home/mymy/rosettainstall/rosetta_src_2020.08.61146_bundle/main/source/bin

Thw full output of running "rosetta.run_tests" was as following.

I am looking forward to getting your advice on what was run for my rosetta installation which can cause the above mentioned  OSError.

Best wishes,

Smith

------

$ rosetta.run_tests
Running Rosetta refinement tests
/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.pdb
/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.mtz
phenix.rosetta_refine /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.pdb /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2

============================== Collecting inputs ==============================


                   ----------Processing X-ray data----------                  

F-obs:
  /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
Miller array info: /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/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:
  /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
Miller array info: /home/mymy/phenix11914122installdir/phenix-1.19.1-4122/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)----------                 


  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/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: 0.03, per 1000 atoms: 0.45
  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 added/changed 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 new custom angles: 0
    Total number of changed 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
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed 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 new custom angles: 0
    Total number of changed 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                : Auto  - 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: 0.01
  Conformation dependent library (CDL) restraints added in 2.0 milliseconds
 
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  12

  Time building geometry restraints manager: 0.00 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 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A   7 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A   7 "   -0.001 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=" 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=" 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    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)=0.1750 0.1754 0.1716 n_refl.: 493
         remove outliers: r(all,work,free)=0.1750 0.1754 0.1716 n_refl.: 493
|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06  % free)--------------|
|                                                                             |
| r_work= 0.1754 r_free= 0.1716 coordinate error (max.-lik. estimate): -0.00 A|
|                                                                             |
| normalized target function (ml) (work): 3.004917                            |
| target function (ml) not normalized (work): 1421.325691                     |
| target function (ml) not normalized (free): 68.085674                       |
|-----------------------------------------------------------------------------|

End of input processing
Traceback (most recent call last):
  File "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 315, in <module>
    run(sys.argv[1:], create_dir=True)
  File "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 144, in run
    scripts_cmd = phenix.rosetta.refine.find_scripts_command()
  File "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/rosetta/refine.py", line 31, in find_scripts_command
    return find_rosetta_command("rosetta_scripts.python.", **kwds)
  File "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/rosetta/refine.py", line 68, in find_rosetta_command
    rosetta_cmd = search_path(rosetta_bin)
  File "/home/mymy/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/rosetta/refine.py", line 49, in search_path
    for node in os.listdir(path) :
OSError: [Errno 2] No such file or directory: '/home/mymy/rosettainstall/rosetta_src_2020.08.61146_bundle/main/source/bin'

 

Post Situation: 
Tue, 2021-03-09 06:11
Smith Lee