RosettaCommons - Phenix / MR Rosetta

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Rosetta 3 - General

Post Situation:

Segfault error while running MR Rosetta in Phenix

memilton — Thu, 16 Dec 2021 17:09:19 +0000

Hello,

In the middle of my MR Rosetta run I got a "Failed to run REBUILD" error. I am at a completely loss for how to solve this problem. Error logs are attached.

I am running rosetta_src_2021.16.61629_bundle on Phenix 1.19.2-4158. I did notice the Phenix instructions for installing Rosetta mention using Rosetta version 3.10 or later, is that the reason for the fail?

Thank you!

Attachment	Size
rebuild.log	145.9 KB
ROSETTA_CRASH.log	4.07 KB

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Post Situation:

Forums:

Rosetta 3 - Applications

rosetta for phenix directory cannot be found error

Smith Lee — Tue, 09 Mar 2021 14:11:48 +0000

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'

Category:

Forums:

Post Situation:

rosetta for phenix directory cannot be found error

Smith Lee — Tue, 09 Mar 2021 14:11:27 +0000

Dear All,

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

------

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

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

Test (R-free flags) flag value: 1

----------Processing PDB file(s)----------

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

Time building geometry restraints manager: 0.00 seconds

NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.

============================== Scattering factors =============================

----------X-ray scattering dictionary----------

----------F(model) initialization----------

Category:

Forums:

Post Situation:

Problems with Installing and Running MR Rosetta 3.10

Priscilla Masamba — Sun, 18 Aug 2019 21:15:48 +0000

I am having a serious challenge running MR Rosetta3.10. Everytime i run it, an error written "sub-process failed" pops up and when i check the log file it indicates that it is looking for a particular file eg score3.wts. Once i get that file linked and run it again, the same error pops up again looking for another set of files e.g ncaa.rotamer.libraries which i do have. This has happened three times with different file searched and it is quite monotonous because my runs take over 18 hours only to receive error messages at the end of the day. My computer technician has told me that it seems like the database is not linked or meged with the Rosetta3.10 source code. How can this problem be fixed? Please do assist...

Priscilla

Category:

Forums:

Post Situation:

Error 1: private field

foggyfoggyfoggy — Thu, 09 May 2019 01:35:10 +0000

Dear All,

I met such kind of error informaiton when I tried to excute the Rosetta in my mac pro by running the command "rosetta.build_phenix_interface nproc=2" .

Can anyone tell me how to solve this issue?

Many thanks.

Liang

clang++ -o build/src/release/macos/18.5/64/x86/clang/10.0/python/protocols/match/output/PDBWriter.os -c -std=c++11 -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/10.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/PDBWriter.cc
In file included from src/protocols/mpi_refinement/WorkUnit_Loop.cc:15:
src/protocols/mpi_refinement/WorkUnit_Loop.hh:140:7: error: private field
'kicclose_' is not used [-Werror,-Wunused-private-field]
bool kicclose_;
^
1 error generated.
scons: *** [build/src/release/macos/18.5/64/x86/clang/10.0/python/protocols/mpi_refinement/WorkUnit_Loop.os] Error 1
scons: building terminated because of errors.

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Forums:

Post Situation:

Change in Gibbs free energy (delta delta G) of RNA

wrshoemaker — Thu, 26 Jan 2017 23:47:43 +0000

Hello,

I'm trying to load a .pdb file for an RNA molecule, change a single base in the molecule, and calculate the change in free energy. I was looking at this tutorial (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf) and it doesn't work with newer versions of PyRosetta. Has anyone else done something like this? The documentation hasn't been very helpful so far for RNA (though it's relatively extensive for protein).

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PyRosetta - Applications

Post Situation:

rosetta_scripts_BOGUS coords warning message

Karol — Tue, 13 Dec 2016 10:35:37 +0000

Hi,

I am using rosetta scripts to build a protein into electron density.

However, I am getting some warning messages, which relate to my CYX residues. I understand the message itself, but I don't know why it appears, what it means to my structure and whether I should be worried about it. As I said, I have several CYS residues, which I mutated to CYX (CYX name in PDB file) and when I start my calculations I am getting the following warning message for all CYX residues:

core.chemical.AtomICoor: Warning from IcoorAtomID::xyz(): ICoorAtomID xyz depends on invalid residue connection, returning BOGUS coords (null vector): this_rsd= CYX 352 connid= 3 partner_seqpos= 0
core.chemical.AtomICoor: Warning from IcoorAtomID::xyz(): ICoorAtomID xyz depends on invalid residue connection, returning BOGUS coords (null vector): this_rsd= CYX 355 connid= 3 partner_seqpos= 0

... and so on

core.conformation.Conformation: Failed to find a residue connection for residue 352 with connection point 3
core.conformation.Conformation: Connecting residues: 355 ( CYX ) and 399 ( CYX ) at atoms SG and SG

... and so on

The weirdest thing is that this message appears only when I submit my job in a threaded mode. When I run it on a single core, I don't have this kind of problem.

I am using Rosetta version: rosetta_bin_linux_2016.32.58837_bundle

Flags below:

rosetta_scripts.linuxgccrelease \
 -database database/ \
 -in::file::PDB.pdb \
 -parser::protocol xml.xml \
 -auto_setup_metals \
 -detect_disulf false \
 -extra_res_fa CYX.params \
 -relax:min_type lbfgs_armijo_nonmonotone \
 -default_max_cycles 200 \
 -relax:jump_move true \
 -edensity:mapreso X \
 -edensity::cryoem_scatterers \
 -crystal_refine \

Any comments will be greatly appreciated

Thanks,

Karl

Category:

Forums:

Rosetta 3 - General

Post Situation:

refining crystal structure using phenix without CIF file

banshee — Fri, 09 Sep 2016 08:14:21 +0000

can one refine a crystal structure which has a ligand with just the mtz file? no cif file for the ligand?

or would that be meaningless result?

thank you.

Category:

Forums:

Rosetta 3 - Applications

Post Situation:

Cryo-EM: problem with RosettaCM using multiple template models as input

Karol — Mon, 29 Aug 2016 12:26:47 +0000

Hi,

First of all, I am not sure about the category of my post, but the "Phenix/MR rosetta" category seems to be the most relevant, considering the topic of this post.

I have been folllowing the cryo-EM tutorial from 2015 to produce a model, which would be derived from the fragments of multiple templates and nicely fit to cryo-EM map. However, all produced models are out of density. I understand that the purpose of this protocol is to perform a more exhaustive sampling, but still several top-scored models are simply out of density, not even close. The problem is with both ccp4 and mrc maps.

Templates are aligned to the density. I checked in both COOT and Chimera, so it is not a problem of headers...I think.

Adding -relax::constrain_relax_to_start_coords flag with different values of of cst improve, but do not solve the problem.

Any suggestions?

rosetta_scripts.linuxgccrelease \
 -database database \
 -in::file::fasta fasta.fasta \
 -parser::protocol xml.xml \
 -edensity::mapfile mrc.mrc \
 -edensity::mapreso 4.3 \
 -edensity::cryoem_scatterers \
 -relax:minimize_bond_angles \
 -relax:min_type lbfgs_armijo_nonmonotone \
 -relax:jump_move true \
 -relax:default_repeats 2 \
 -default_max_cycles 200 \
 -nstruct 50 \
 -out::suffix _ref2_$1 \

<ROSETTASCRIPTS> 
	<SCOREFXNS> 
		<stage1 weights="score3">
			<Reweight scoretype=atom_pair_constraint weight=0.25/> 
		</stage1>
		<stage2 weights="score4_smooth_cart"> 
			<Reweight scoretype=atom_pair_constraint weight=0.25/> 
		</stage2> 
		<fullatom weights="talaris2013_cart"> 
			<Reweight scoretype=atom_pair_constraint weight=0.25/> 
		</fullatom> 
	</SCOREFXNS> 
	<MOVERS>¨
		<Hybridize name=hybridize stage1_scorefxn=stage1 stage2_scorefxn=stage2 fa_scorefxn=fullatom batch=1>
			<Template pdb="thr_1.pdb" weight=1.0 cst_file="AUTO"/> 
			<Template pdb="thr_2.pdb" weight=1.0 cst_file="AUTO"/>
			<Template pdb="thr_3.pdb" weight=1.0 cst_file="AUTO"/>
			<Template pdb="thr_4.pdb" weight=1.0 cst_file="AUTO"/> 
		</Hybridize> 
	</MOVERS> 
	<PROTOCOLS> 
		<Add mover=hybridize/> 
	</PROTOCOLS> 
</ROSETTASCRIPTS>

2.) Additionally, I am not sure whether the tutorial itself is up to date. According to the tutorial, the "AUTO" flag should be "auto", but actually it should not be.

When I change to "auto" I get error = [ERROR] Unable to open constraints file: auto

3.) Finally, which flags specify rescoring againts density? Shouldn't we use any density scoring function? I mean, does the hybridizer follows any density data when building structures? The main script file also does not contain any density function.

thank you

Karl

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Forums:

Rosetta 3 - General

Post Situation: