rosetta for phenix directory cannot be found error

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’