[phenixbb] errors when disabling Rfree
Pavel Afonine
pafonine at lbl.gov
Sun Jan 2 21:52:54 PST 2011
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, chene at umbi.umd.edu 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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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