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

Yamei Yu ymyuxtal at gmail.com
Wed Nov 26 17:52:47 PST 2014


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
           ymyuxtal at 163.com
           yamei_yu at scu.edu.cn

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