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Hi Chen,<br>
<br>
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).<br>
<br>
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.<br>
<br>
So, following Peter's suggestion: the best fix for you now is to use
free-R set of reflections in refinement.<br>
<br>
Pavel.<br>
<br>
<br>
On 12/23/10 10:06 AM, <a class="moz-txt-link-abbreviated" href="mailto:chene@umbi.umd.edu">chene@umbi.umd.edu</a> wrote:
<blockquote cite="mid:f6ce0418ba1.4d13495a@umbi.umd.edu" type="cite">Dear
Phenixers, <br>
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.<br>
I wonder how to fix this problem?<br>
Thanks<br>
Chen<br>
<br>
Traceback (most recent call last):<br>
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module><br>
command_line.run(command_name="phenix.refine",
args=sys.argv[1:])<br>
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 103, in run<br>
map_manger.write_files()<br>
File
"/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1281, in write_files<br>
fmodel = self.refine_object.fmodels.fmodel_xray(), params =
mtz_mc)<br>
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py",
line 290, in map_coefficients_from_fmodel<br>
centrics_pre_scale = params.centrics_pre_scale)<br>
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1780, in map_coefficients<br>
w2 = w2)<br>
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1695, in map_coefficients<br>
sigmaa_object = self.sigmaa_object(
detwinned_data=dt_f_obs,f_model_data=tmp_f_model,
tmp_free=tmp_free,forced_update=True)<br>
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py",
line 1504, in sigmaa_object<br>
kernel_width_free_reflections=200,<br>
File
"/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py",
line 131, in __init__<br>
raise RuntimeError("No free reflections.")<br>
RuntimeError: No free reflections.<br>
<br>
<br>
Chen Chen, PhD, Research Associate<br>
Center for Advanced Research in Biotechnology (CARB),<br>
University of Maryland Biotechnology Institute (UMBI),<br>
9600 Gudelsky Drive, Rockville, MD 20850<br>
240-314-6122 <br>
<br>
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