[phenixbb] Not a suitable array of R-free flags:

[Pavel Afonine]

Hi Yamei,

could you please send me files necessary to reproduce this problem? From 
your description it isn't clear for me what's wrong..

Pavel

On 11/26/14 5:52 PM, Yamei Yu wrote:
> Dear all,
>
> I use phenix.refine to refine a structure.
>
>  Firstly, I used --dryrun to generate an .eff file. The command is 
> "phenix.refine --dry_run 7_44.mtz 7_44.pdb 
> refinement.input.xray_data.r_free_flags.generate=True 
> refinement.input.xray_data.r_free_flags.max_free=1000”
>  Then I use run the program by typing “phenix.refine 
> 7_44_refine_001.eff” It runs correct!
>
> After that I use coot to modulate some parts of the structure, then I 
> want to refine the structure again. I type “ phenix.refine 
>  7_44_refine_002.def”
> This time I got the following error message:
>
> Not a suitable array of R-free flags: 
> refinement.input.xray_data.r_free_flags.label=R-free-flags
>
> Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: 
> refinement.input.xray_data.r_free_flags.label=R-free-flags
> To override the suitability test define: 
> refinement.input.xray_data.r_free_flags.disable_suitability_test=True
>
> I checked the generated file by phenix “7_44_refine_data.mtz” I 
> does contain a column labeled as R-free-flags. I paste part if it below.
> * Space group = 'P1' (number     1)
>
>
>
>  OVERALL FILE STATISTICS for resolution range   0.000 -   0.277
>  =======================
>
>
>  Col Sort    Min    Max    Num %     Mean     Mean   Resolution   Type 
> Column
>  num order               Missing complete          abs.   Low    High 
>       label
>
>    1 ASC    -32      31      0 100.00     -2.2     11.9  49.44   1.90 
>   H  H
>    2 NONE   -46      45      0 100.00     -2.5     17.8  49.44   1.90 
>   H  K
>    3 NONE     0      49      0 100.00     18.8     18.8  49.44   1.90 
>   H  L
>    4 NONE    0.9   271.3     0 100.00    26.52    26.52  49.44   1.90 
>   F  F-obs
>    5 NONE    0.2     5.1     0 100.00     1.25     1.25  49.44   1.90 
>   Q  SIGF-obs
>    6 NONE    0.0     1.0     0 100.00     0.01     0.01  49.44   1.90 
>   I  R-free-flags
>
>
>  No. of reflections used in FILE STATISTICS   143215
>
> Then I regenerate a new mtz file with FreeRflag by XDSCONT, then I 
> revise the .def file accordingly and rerun the program. I got same 
> error message:Not a suitable array of R-free flags: 
> refinement.input.xray_data.r_free_flags.label=FreeRflag
>
> Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: 
> refinement.input.xray_data.r_free_flags.label=FreeRflag
> To override the suitability test define: 
> refinement.input.xray_data.r_free_flags.disable_suitability_test=True
>
> I checked my new mtz file, it dose contain a column labeled as FreeRflag
>
> Why there is an error message? How to solve it?
>
> Thank you so much!!
>
> Best wishes!
>
> yamei
>
> ************************************************
>
> Yamei Yu
> State Key Laboratory of Biotherapy／Collaborative Innovation
> Center of Biotherapy,
> West China Hospital,
> Sichuan University,Chengdu,610041, P.R.China
> Tel: 15882013485
> Email: ymyuxtal at gmail.com <mailto:ymyuxtal at gmail.com>
> ymyuxtal at 163.com <mailto:ymyuxtal at 163.com>
> yamei_yu at scu.edu.cn <mailto:yamei_yu at scu.edu.cn>
>
>
>
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