Re: [phenixbb] phenix.rosetta_refine on OS X?

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 wrote:

Hi Ben,

I have! What would you like to know?

Best, Luca

...

On Dec 18, 2013, at 19:47, "Ben Eisenbraun" 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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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