[phenixbb] errors when disabling Rfree

Peter Zwart PHZwart at lbl.gov
Thu Dec 23 15:34:53 PST 2010


One way to fix it would be to use R-free of course ....

Why did you disable the use of cross validation?

P

On 23 December 2010 10:06,  <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
>
>



-- 
-----------------------------------------------------------------
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-----------------------------------------------------------------



More information about the phenixbb mailing list