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

Thanks- now, of course, I get a new error after it gets started. Any help would be great. [mcdbx-horowsah:120813/1to8p4122fromqinping/phenix_refine] horowsah% phenix.rosetta_refine zn-ref2_noalt2.pdb 1to8p4122znfromqingping_refine_data.mtz protocol=hires Output directory: /Users/horowsah/Documents/Bardwell Lab Work/spy/xtalstrucs/120813/1to8p4122fromqinping/phenix_refine/rosetta_9 =========================== 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---------- Warning: temporarily removing residue X 227 IMD Warning: temporarily removing residue X 228 IMD Warning: temporarily removing residue X 229 IMD /rosetta/rosetta_2013wk49_bundle/main/source ----------Loading model and data---------- =========================== ROSETTA X-ray refinement ========================== |-starting model--------------------------------------------------------------| | target_work(ml) = 5.09382 r_work = 0.2295 r_free = 0.2807 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.00 % favored = 98.22 % Rotamer outliers = 2.10 % C-beta deviations = 0 Clashscore = 1.78 Molprobity score = 1.18 Generating 5 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: ERROR: ERROR: Unused "free" argument specified: Lab 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 307, in __init__ self.run_jobs() File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py", line 372, in run_jobs check_result(result) File "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py", line 363, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Scott On Thu, Dec 19, 2013 at 10:16 AM, Nathaniel Echols wrote:

On Thu, Dec 19, 2013 at 7:08 AM, Scott Horowitz wrote:

...

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:

... 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

Your PDB file and your data file have different space groups - usually this means that either the PDB file is missing symmetry entirely and gets treated as a P1 box, or the PDB file specifies the screw axes while the data file only specifies the point group (for instance, P212121 versus P222). This is something we normally try to handle more automatically but the input handler for the Rosetta refinement is somewhat less flexible at the moment. I'll fix this, but it should run okay if you ensure that the space group is unambiguously specified in both files.

-Nat

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- 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