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'
