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<p>Dear Scientific Community, I am struggling installing rosetta on
ubuntu 18.04.1 LTS and phenix 1.14-3211-000.<br>
</p>
<p>I followed the instruction as in</p>
<p><a class="moz-txt-link-freetext" href="https://www.phenix-online.org/documentation/reference/rosetta_install.html">https://www.phenix-online.org/documentation/reference/rosetta_install.html</a><br>
</p>
<p>the provided link
<a class="moz-txt-link-freetext" href="https://c4c.uwc4c.com/express_license_technologies/rosetta">https://c4c.uwc4c.com/express_license_technologies/rosetta</a> <br>
</p>
<p>gives an "This site can't be reached error"</p>
<p>Therfore I went to <a class="moz-txt-link-freetext" href="https://www.rosettacommons.org/software">https://www.rosettacommons.org/software</a></p>
<p>and downloaded <br>
</p>
<p><img src="cid:part1.2895D56B.338BAF45@univie.ac.at" alt=""
height="56" width="341"></p>
<p>and unpacked in
/home/g/programs/rosetta_src_2016.32.58837_bundle/</p>
<p>I added the line<br>
</p>
<p>export
PHENIX_ROSETTA_PATH=/home/g/programs/rosetta_src_2016.32.58837_bundle/</p>
<p>to .bashrc</p>
<p>running<br>
</p>
<p>rosetta.build_phenix_interface nproc=8</p>
<p>I can't remember if it was fine. Running it now gives</p>
<p>g@glap:~$ rosetta.build_phenix_interface nproc=8<br>
Substituting phenix.python into build shell scripts<br>
update_options.sh<br>
update_ResidueType_enum_files.sh<br>
Applying patch<br>
patching file source/src/core/kinematics/tree/Atom.hh<br>
Reversed (or previously applied) patch detected! Assume -R? [n] <br>
</p>
<p><b>pressing n</b></p>
<p>Apply anyway? [n] n<br>
Skipping patch.<br>
2 out of 2 hunks ignored -- saving rejects to file
source/src/core/kinematics/tree/Atom.hh.rej<br>
patching file source/src/core/kinematics/tree/Atom_.cc<br>
Hunk #1 FAILED at 817.<br>
1 out of 1 hunk FAILED -- saving rejects to file
source/src/core/kinematics/tree/Atom_.cc.rej<br>
patching file source/src/core/kinematics/tree/Atom_.hh<br>
Hunk #1 FAILED at 467.<br>
1 out of 1 hunk FAILED -- saving rejects to file
source/src/core/kinematics/tree/Atom_.hh.rej<br>
patching file source/src/core/kinematics/tree/BondedAtom.cc<br>
Hunk #1 FAILED at 542.<br>
1 out of 1 hunk FAILED -- saving rejects to file
source/src/core/kinematics/tree/BondedAtom.cc.rej<br>
patching file source/src/core/kinematics/tree/BondedAtom.hh<br>
Hunk #1 FAILED at 259.<br>
1 out of 1 hunk FAILED -- saving rejects to file
source/src/core/kinematics/tree/BondedAtom.hh.rej<br>
patch unexpectedly ends in middle of line<br>
<br>
Phenix modules found :
/usr/local/phenix-1.14-3211/modules/phenix<br>
Traceback (most recent call last):<br>
File
"/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py",
line 265, in <module><br>
run(sys.argv[1:])<br>
File
"/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py",
line 225, in run<br>
f=file("dispatcher_include_erraser.sh", "wb")<br>
IOError: [Errno 13] Permission denied:
'dispatcher_include_erraser.sh'<br>
</p>
<p><b>running the run test gives following.</b><br>
</p>
<p>lap:~$ rosetta.run_tests<br>
Running Rosetta refinement tests<br>
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.pdb<br>
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz<br>
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<br>
<br>
============================== Collecting inputs
==============================<br>
<br>
<br>
----------Processing X-ray
data---------- <br>
<br>
F-obs:<br>
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X<br>
Miller array info:
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X<br>
Observation type: xray.amplitude<br>
Type of data: double, size=495<br>
Type of sigmas: double, size=495<br>
Number of Miller indices: 495<br>
Anomalous flag: False<br>
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)<br>
Space group: P 1 21 1 (No. 4)<br>
Systematic absences: 0<br>
Centric reflections: 199<br>
Resolution range: 22.4416 1.80066<br>
Completeness in resolution range: 0.895118<br>
Completeness with d_max=infinity: 0.895118<br>
Wavelength: 1.0000<br>
<br>
Number of F-obs in resolution range: 495<br>
Number of F-obs<0 (these reflections will be rejected): 0<br>
Number of F-obs=0 (these reflections will be used in refinement):
0<br>
Refinement resolution range: d_max = 22.4416<br>
d_min = 1.8007<br>
<br>
R-free flags:<br>
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags<br>
Miller array info:
/usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags<br>
Observation type: None<br>
Type of data: int, size=495<br>
Type of sigmas: None<br>
Number of Miller indices: 495<br>
Anomalous flag: False<br>
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)<br>
Space group: P 1 21 1 (No. 4)<br>
Systematic absences: 0<br>
Centric reflections: 199<br>
Resolution range: 22.4416 1.80066<br>
Completeness in resolution range: 0.895118<br>
Completeness with d_max=infinity: 0.895118<br>
Wavelength: 1.0000<br>
<br>
Test (R-free flags) flag value: 1<br>
<br>
Number of work/free reflections by resolution:<br>
work free %free<br>
bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%<br>
bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%<br>
bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%<br>
bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%<br>
bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%<br>
bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%<br>
bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%<br>
bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%<br>
bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%<br>
bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%<br>
overall 475 20 4.0%<br>
<br>
----------Processing PDB
file(s)---------- <br>
<br>
Monomer Library directory:<br>
"/usr/local/phenix-1.14-3211/modules/chem_data/mon_lib"<br>
Total number of atoms: 66<br>
Number of models: 1<br>
Model: ""<br>
Number of chains: 2<br>
Chain: "A"<br>
Number of atoms: 59<br>
Number of conformers: 1<br>
Conformer: ""<br>
Number of residues, atoms: 7, 59<br>
Classifications: {'peptide': 7}<br>
Modifications used: {'COO': 1}<br>
Link IDs: {'TRANS': 6}<br>
Chain: " "<br>
Number of atoms: 7<br>
Number of conformers: 1<br>
Conformer: ""<br>
Number of residues, atoms: 7, 7<br>
Classifications: {'water': 7}<br>
Link IDs: {None: 6}<br>
Time building chain proxies: 0.13, per 1000 atoms: 1.97<br>
Number of scatterers: 66<br>
At special positions: 0<br>
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)<br>
Space group: P 1 21 1 (No. 4)<br>
Number of sites at special positions: 0<br>
Number of scattering types: 3<br>
Type Number sf(0)<br>
O 21 8.00<br>
N 12 7.00<br>
C 33 6.00<br>
sf(0) = scattering factor at diffraction angle 0.<br>
<br>
Number of disulfides: simple=0, symmetry=0<br>
Custom bonds:<br>
Warning: Ignoring bond with distance_ideal = None:<br>
atom_selection_1 = None<br>
atom_selection_2 = None<br>
Total number of custom bonds: 0<br>
Custom angles:<br>
Warning: Ignoring angle with angle_ideal = None:<br>
atom_selection_1 = None<br>
atom_selection_2 = None<br>
atom_selection_3 = None<br>
Total number of custom angles: 0<br>
Custom dihedrals:<br>
Warning: Ignoring dihedral with angle_ideal = None:<br>
atom_selection_1 = None<br>
atom_selection_2 = None<br>
atom_selection_3 = None<br>
atom_selection_4 = None<br>
Total number of custom dihedrals: 0<br>
Custom planarities:<br>
Warning: Ignoring planarity with with sigma <= 0:<br>
atom_selection = None<br>
None<br>
Total number of custom planarities: 0<br>
Custom parallelities:<br>
Warning: Ignoring parallelity with empty atom selection.<br>
Total number of custom parallelities: 0<br>
<br>
Automatic linking<br>
Parameters for automatic linking<br>
Linking & cutoffs<br>
Metal : False - 3.50<br>
Amimo acid : False - 1.90<br>
Carbohydrate : True - 1.99<br>
Ligands : True - 1.99<br>
Small molecules : False - 1.98<br>
Amino acid - RNA/DNA : False<br>
<br>
Number of custom bonds: simple=0, symmetry=0<br>
Time building additional restraints: 0.02<br>
Conformation dependent library (CDL) restraints added in 3.5
milliseconds<br>
<br>
Adding C-beta torsion restraints...<br>
Number of C-beta restraints generated: 12<br>
<br>
Time building geometry restraints manager: 0.02 seconds<br>
<br>
NOTE: a complete listing of the restraints can be obtained by
requesting<br>
output of .geo file.<br>
<br>
Histogram of bond lengths:<br>
1.23 - 1.29: 13<br>
1.29 - 1.36: 11<br>
1.36 - 1.42: 7<br>
1.42 - 1.49: 6<br>
1.49 - 1.55: 22<br>
Bond restraints: 59<br>
Sorted by residual:<br>
bond pdb=" N GLY A 1 "<br>
pdb=" CA GLY A 1 "<br>
ideal model delta sigma weight residual<br>
1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01<br>
bond pdb=" CA GLN A 4 "<br>
pdb=" C GLN A 4 "<br>
ideal model delta sigma weight residual<br>
1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00<br>
bond pdb=" N GLN A 4 "<br>
pdb=" CA GLN A 4 "<br>
ideal model delta sigma weight residual<br>
1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00<br>
bond pdb=" CA ASN A 2 "<br>
pdb=" C ASN A 2 "<br>
ideal model delta sigma weight residual<br>
1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00<br>
bond pdb=" CA ASN A 6 "<br>
pdb=" C ASN A 6 "<br>
ideal model delta sigma weight residual<br>
1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00<br>
... (remaining 54 not shown)<br>
<br>
Histogram of bond angle deviations from ideal:<br>
107.05 - 110.59: 8<br>
110.59 - 114.13: 19<br>
114.13 - 117.67: 11<br>
117.67 - 121.21: 23<br>
121.21 - 124.75: 18<br>
Bond angle restraints: 79<br>
Sorted by residual:<br>
angle pdb=" N ASN A 3 "<br>
pdb=" CA ASN A 3 "<br>
pdb=" C ASN A 3 "<br>
ideal model delta sigma weight residual<br>
108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00<br>
angle pdb=" N GLN A 4 "<br>
pdb=" CA GLN A 4 "<br>
pdb=" C GLN A 4 "<br>
ideal model delta sigma weight residual<br>
108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00<br>
angle pdb=" CA GLN A 4 "<br>
pdb=" C GLN A 4 "<br>
pdb=" O GLN A 4 "<br>
ideal model delta sigma weight residual<br>
120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00<br>
angle pdb=" CA GLN A 5 "<br>
pdb=" C GLN A 5 "<br>
pdb=" O GLN A 5 "<br>
ideal model delta sigma weight residual<br>
120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00<br>
angle pdb=" C GLN A 4 "<br>
pdb=" N GLN A 5 "<br>
pdb=" CA GLN A 5 "<br>
ideal model delta sigma weight residual<br>
123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00<br>
... (remaining 74 not shown)<br>
<br>
Histogram of dihedral angle deviations from ideal:<br>
0.04 - 14.51: 26<br>
14.51 - 28.98: 5<br>
28.98 - 43.45: 1<br>
43.45 - 57.92: 1<br>
57.92 - 72.39: 1<br>
Dihedral angle restraints: 34<br>
sinusoidal: 15<br>
harmonic: 19<br>
Sorted by residual:<br>
dihedral pdb=" CA ASN A 3 "<br>
pdb=" C ASN A 3 "<br>
pdb=" N GLN A 4 "<br>
pdb=" CA GLN A 4 "<br>
ideal model delta harmonic sigma weight residual<br>
180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00<br>
dihedral pdb=" CB GLN A 5 "<br>
pdb=" CG GLN A 5 "<br>
pdb=" CD GLN A 5 "<br>
pdb=" OE1 GLN A 5 "<br>
ideal model delta sinusoidal sigma weight residual<br>
0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00<br>
dihedral pdb=" CB GLN A 4 "<br>
pdb=" CG GLN A 4 "<br>
pdb=" CD GLN A 4 "<br>
pdb=" OE1 GLN A 4 "<br>
ideal model delta sinusoidal sigma weight residual<br>
0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00<br>
... (remaining 31 not shown)<br>
<br>
Histogram of chiral volume deviations from ideal:<br>
0.000 - 0.024: 1<br>
0.024 - 0.047: 1<br>
0.047 - 0.071: 1<br>
0.071 - 0.094: 1<br>
0.094 - 0.118: 2<br>
Chirality restraints: 6<br>
Sorted by residual:<br>
chirality pdb=" CA GLN A 5 "<br>
pdb=" N GLN A 5 "<br>
pdb=" C GLN A 5 "<br>
pdb=" CB GLN A 5 "<br>
both_signs ideal model delta sigma weight residual<br>
False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01<br>
chirality pdb=" CA ASN A 6 "<br>
pdb=" N ASN A 6 "<br>
pdb=" C ASN A 6 "<br>
pdb=" CB ASN A 6 "<br>
both_signs ideal model delta sigma weight residual<br>
False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01<br>
chirality pdb=" CA ASN A 2 "<br>
pdb=" N ASN A 2 "<br>
pdb=" C ASN A 2 "<br>
pdb=" CB ASN A 2 "<br>
both_signs ideal model delta sigma weight residual<br>
False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01<br>
... (remaining 3 not shown)<br>
<br>
Planarity restraints: 13<br>
Sorted by residual:<br>
delta sigma weight
rms_deltas residual<br>
plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03
9.66e-03 1.87e+00<br>
pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03<br>
pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03<br>
pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03<br>
pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03<br>
pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03<br>
pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03<br>
pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03<br>
delta sigma weight
rms_deltas residual<br>
plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03
1.19e-02 1.42e+00<br>
pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03<br>
pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03<br>
pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03<br>
delta sigma weight
rms_deltas residual<br>
plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03
1.09e-02 1.18e+00<br>
pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03<br>
pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03<br>
pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03<br>
... (remaining 10 not shown)<br>
<br>
Histogram of nonbonded interaction distances:<br>
2.53 - 3.00: 50<br>
3.00 - 3.48: 107<br>
3.48 - 3.95: 243<br>
3.95 - 4.42: 255<br>
4.42 - 4.90: 523<br>
Nonbonded interactions: 1178<br>
Sorted by model distance:<br>
nonbonded pdb=" OH TYR A 7 "<br>
pdb=" O HOH 11 "<br>
model vdw sym.op.<br>
2.525 2.440 -x+1,y-1/2,-z+1<br>
nonbonded pdb=" O HOH 11 "<br>
pdb=" OH TYR A 7 "<br>
model vdw sym.op.<br>
2.525 2.440 -x+1,y+1/2,-z+1<br>
nonbonded pdb=" O HOH 14 "<br>
pdb=" O HOH 13 "<br>
model vdw sym.op.<br>
2.634 2.440 x,y-1,z<br>
nonbonded pdb=" O HOH 13 "<br>
pdb=" O HOH 14 "<br>
model vdw sym.op.<br>
2.634 2.440 x,y+1,z<br>
nonbonded pdb=" N GLY A 1 "<br>
pdb=" O GLY A 1 "<br>
model vdw<br>
2.665 2.496<br>
... (remaining 1173 not shown)<br>
<br>
NOTE: a complete listing of the restraints can be obtained by
requesting<br>
output of .geo file.<br>
<br>
============================== Scattering factors
=============================<br>
<br>
<br>
----------X-ray scattering
dictionary---------- <br>
<br>
Number of scattering types: 3<br>
Type Number sf(0) Gaussians<br>
O 21 7.97 2<br>
N 12 6.97 2<br>
C 33 5.97 2<br>
sf(0) = scattering factor at diffraction angle 0.<br>
<br>
Number of scatterers: 66<br>
At special positions: 0<br>
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)<br>
Space group: P 1 21 1 (No. 4)<br>
<br>
----------F(model)
initialization---------- <br>
<br>
Twinning will be detected automatically.<br>
start: r(all,work,free)=0.2072 0.2084 0.1924
n_refl.: 495<br>
re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924
n_refl.: 495<br>
remove outliers: r(all,work,free)=0.2103 0.2117 0.1924
n_refl.: 493<br>
bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728
n_refl.: 493<br>
remove outliers: r(all,work,free)=0.1755 0.1758 0.1728
n_refl.: 493<br>
|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 %
free)--------------|<br>
|
|<br>
| r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik.
estimate): -0.00 A|<br>
|
|<br>
| normalized target function (ml) (work):
2.637727 |<br>
| target function (ml) not normalized (work):
1247.644901 |<br>
| target function (ml) not normalized (free):
60.766973 |<br>
|-----------------------------------------------------------------------------|<br>
<br>
End of input processing<br>
Sorry: <br>
The RosettaScripts executable could not be located. Please
set the<br>
environmental variable PHENIX_ROSETTA_PATH or add the
appropriate<br>
directory to your PATH environment variable.<br>
<br>
</p>
<p><b>I am grateful for any advice.</b></p>
<p><b>Best regards, Georg.</b><br>
</p>
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