[phenixbb] phenix.rosetta_refine on OS X?

Scott Horowitz horowsah at umich.edu
Thu Dec 19 07:30:14 PST 2013


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 <nechols at lbl.gov> wrote:

> On Thu, Dec 19, 2013 at 7:08 AM, Scott Horowitz <horowsah at umich.edu>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
> phenixbb at phenix-online.org
> 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
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