[phenixbb] phenix.rosetta_refine on OS X?

Scott Horowitz horowsah at umich.edu
Thu Dec 19 07:08:02 PST 2013


Well, while we're on this topic, I was just starting to try phenix-rosetta
on a mac, and after following the instructions online I get this error
message:

mcdbx-horowsah:120813/1to8p4122fromqinping/phenix_refine] horowsah%
phenix.rosetta_refine 1to8norm10_refine_17-coot-1nohnoe.pdb
zn-truncate-unique.mtz nproc=4 protocol=hires
Output directory:
  /Users/horowsah/Documents/Bardwell Lab
Work/spy/xtalstrucs/120813/1to8p4122fromqinping/phenix_refine/rosetta_6

=========================== Importing data and flags
==========================


     ----------Scaling input intensities via French-Wilson Method----------


Trying 60 bins...
Number of bins = 60
** Calculating bin mean intensity values for each intensity **
** Total # rejected intensities: 0 **

             ----------Setting up input files for Rosetta----------


/rosetta/rosetta_2013wk49_bundle/main/source

                   ----------Loading model and data----------


Traceback (most recent call last):
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py",
line 330, in <module>
    run(sys.argv[1:], create_dir=True)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py",
line 327, in run
    create_dir=create_dir)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py",
line 127, in __init__
    self.run_rosetta_scripts()
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py",
line 181, in run_rosetta_scripts
    debug=self.params.runtime.debug)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py",
line 287, in __init__
    r_free_flags=r_free_flags)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py",
line 1802, in fmodel_simple
    ro = outliers_rejection,om=optimize_mask, ofp1=False)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py",
line 1788, in get_fmodel
    twin_law       = tl)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py",
line 1707, in fmodel_manager
    n_resolution_bins_output     = n_resolution_bins_output)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/f_model.py",
line 432, in __init__
    if(f_calc is None): f_calc = self.compute_f_calc(miller_array=f_obs)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/f_model.py",
line 518, in compute_f_calc
    exp_table_one_over_step_size = p.exp_table_one_over_step_size)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/miller/__init__.py",
line 1374, in structure_factors_from_scatterers
    algorithm=algorithm)
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/from_scatterers.py",
line 53, in __call__
    algorithm=algorithm) # passing algorithm allows f to decide on CPU/GPU
implementation
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/from_scatterers_fft.py",
line 18, in __init__
    manager, xray_structure, miller_set, algorithm="fft")
  File
"//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/manager.py",
line 234, in __init__
    assert xray_structure.space_group() == miller_set.space_group()
AssertionError


Anybody know what I did wrong?

Thanks,
Scott


On Wed, Dec 18, 2013 at 5:17 PM, Luca Jovine <Luca.Jovine at ki.se> wrote:

> Hi Ben,
>
> I have! What would you like to know?
>
> Best, Luca
>
> > On Dec 18, 2013, at 19:47, "Ben Eisenbraun" <bene at hkl.hms.harvard.edu>
> wrote:
> >
> > Hi All,
> >
> > Has anyone run the Phenix-Rosetta refinement stuff on a Mac yet?
> >
> > Thanks.
> >
> > -ben
> >
> > --
> > | Ben Eisenbraun
> > | SBGrid Consortium                          | http://sbgrid.org       |
> > | Harvard Medical School                     | http://hms.harvard.edu  |
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
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>



-- 
Scott Horowitz, Ph.D.
Research Associate
Howard Hughes Medical Institute

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226
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