Hi Chen,
the crash is not good, I will fix it - it is definitely a bug
specific to twin-refinement (since I know we have a test that runs
refinement without using test reflections but using different
target).
The maps we are typically look at are 2mFo-DFc and mFo-DFc. It is
essential that the coefficients m and D are estimated using proper
unbiased test reflections.
So, following Peter's suggestion: the best fix for you now is to use
free-R set of reflections in refinement.
Pavel.
On 12/23/10 10:06 AM, [email protected] wrote:
Dear
Phenixers,
I have a low resolution twinned data, for which I disabled cross
validation in refinement. The refinement worked and exported the
refined coordinates. However, the phs files for maps are empty and
there were such errors as below. It seems the free set is required
for maps.
I wonder how to fix this problem?
Thanks
Chen
Traceback (most recent call last):
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module>
command_line.run(command_name="phenix.refine",
args=sys.argv[1:])
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 103, in run
map_manger.write_files()
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1281, in write_files
fmodel = self.refine_object.fmodels.fmodel_xray(), params =
mtz_mc)
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py",
line 290, in map_coefficients_from_fmodel
centrics_pre_scale = params.centrics_pre_scale)
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1780, in map_coefficients
w2 = w2)
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1695, in map_coefficients
sigmaa_object = self.sigmaa_object(
detwinned_data=dt_f_obs,f_model_data=tmp_f_model,
tmp_free=tmp_free,forced_update=True)
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1504, in sigmaa_object
kernel_width_free_reflections=200,
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py",
line 131, in __init__
raise RuntimeError("No free reflections.")
RuntimeError: No free reflections.
Chen Chen, PhD, Research Associate
Center for Advanced Research in Biotechnology (CARB),
University of Maryland Biotechnology Institute (UMBI),
9600 Gudelsky Drive, Rockville, MD 20850
240-314-6122
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