[phenixbb] error loading SHELXL HKLF4 reflection file

[jonathan elegheert]

Dear phenix developers,

I am using the one of the latest phenix.refine nightly builds, and I'm 
trying to load a SHELXL .hkl file into phenix;

phenix.refine xxx_refine_004.def xray_data.file_name="/path/xxx.hkl"=hklf4

The "Iobs,SigIobs"labels are well recognized (so the "Merging 
symmetry-equivalent intensities" subroutine works ok), but the necessary 
"=hklf4" or "=intensities" appendage seems to cause problems. The 
strange thing is that in phenix.xtriage, the same command line flag 
works perfectly fine.

Thank you for any pointers!

Jonathan Elegheert
PhD student
Ghent University

--------------

Traceback (most recent call last):
  File "/usr/local/phenix-1.4-95/phenix/phenix/command_line/refine.py", 
line 19, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File 
"/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", 
line 68, in run
    log=log)
  File 
"/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", 
line 245, in __init__
    log                      = self.log)
  File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 
201, in __init__
    self.raw_flags = self.extract_flags(data = self.raw_data)
  File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 
266, in extract_flags
    parameter_scope          = self.flags_parameter_scope)
  File 
"/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", 
line 566, in get_r_free_flags
    miller_arrays = self.get_miller_arrays(file_name=file_name)
  File 
"/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", 
line 406, in get_miller_arrays
    if (os.path.samefile(canonical_file_name, tabulated_file_name)):
  File 
"/usr/local/phenix-1.4-95/build/intel-linux-2.6-x86_64/base/lib/python2.6/posixpath.py", 
line 153, in samefile
    s2 = os.stat(f2)
OSError: [Errno 2] No such file or directory: '/path/xxx.hkl=hklf4'