[phenixbb] errors when disabling Rfree

[Pavel Afonine]

  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
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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