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
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