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Hi <font face="Menlo"><span style="font-size: 14px;">Yamei</span></font>,<br>
<br>
<font face="Menlo"><span style="font-size: 14px;"></span></font>
<div class="moz-cite-prefix">could you please send me files
necessary to reproduce this problem? From your description it
isn't clear for me what's wrong..<br>
<br>
Pavel<br>
<br>
On 11/26/14 5:52 PM, Yamei Yu wrote:<br>
</div>
<blockquote
cite="mid:C5E1FD4C-8E35-4648-9211-5AE51256A486@gmail.com"
type="cite">
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<span style="font-size: 14px;">Dear all,</span>
<div><span style="font-size: 14px;"><br>
</span></div>
<div><span style="font-size: 14px;">I use phenix.refine to refine
a structure.</span></div>
<div><span style="font-size: 14px;"><br>
</span></div>
<div><span style="font-size: 14px;"> Firstly, I used --dryrun to
generate an .eff file. The command is "<span
style="font-family: Menlo;">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</span><font
face="Menlo">”</font></span></div>
<div><span style="font-size: 14px;"> Then I use run the program by
typing “phenix.refine 7_44_refine_001.eff” It runs correct!</span></div>
<div><span style="font-size: 14px;"><br>
</span></div>
<div><span style="font-size: 14px;">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”</span></div>
<div><span style="font-size: 14px;">This time I got the following
error message: </span></div>
<div><span style="font-size: 14px;"><br>
</span></div>
<div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;">Not a suitable array of R-free
flags:
refinement.input.xray_data.r_free_flags.label=R-free-flags</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;">Sorry_Not_a_suitable_array: Not a
suitable array of R-free flags:
refinement.input.xray_data.r_free_flags.label=R-free-flags</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;">To override the suitability test
define:
refinement.input.xray_data.r_free_flags.disable_suitability_test=True</span></div>
</div>
<div><span style="font-size: 14px;"><br>
</span></div>
<div><span style="font-size: 14px;">I checked the generated file
by phenix “<font face="Menlo">7_44_refine_data.mtz” I
does contain a column labeled as R-free-flags. I paste part
if it below.</font></span></div>
<div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;">* Space group = 'P1' (number 1)</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> OVERALL FILE STATISTICS for
resolution range 0.000 - 0.277</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> ======================= </span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> Col Sort Min Max Num
% Mean Mean Resolution Type Column</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> num order Missing
complete abs. Low High label </span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 1 ASC -32 31 0
100.00 -2.2 11.9 49.44 1.90 H H</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 2 NONE -46 45 0
100.00 -2.5 17.8 49.44 1.90 H K</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 3 NONE 0 49 0
100.00 18.8 18.8 49.44 1.90 H L</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 4 NONE 0.9 271.3 0
100.00 26.52 26.52 49.44 1.90 F F-obs</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 5 NONE 0.2 5.1 0
100.00 1.25 1.25 49.44 1.90 Q SIGF-obs</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> 6 NONE 0.0 1.0 0
100.00 0.01 0.01 49.44 1.90 I R-free-flags</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo; min-height: 13px;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"> No. of reflections used in FILE
STATISTICS 143215</span></div>
</div>
<div style="margin: 0px; font-family: Menlo;"><span
style="font-size: 14px;"><br>
</span></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">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:</span></font><span style="font-family: Menlo;
font-size: 11px;">Not a suitable array of R-free flags:
refinement.input.xray_data.r_free_flags.label=FreeRflag</span></div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;
min-height: 13px;"><br>
</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Sorry_Not_a_suitable_array:
Not a suitable array of R-free flags:
refinement.input.xray_data.r_free_flags.label=FreeRflag</div>
<div style="margin: 0px;"><span style="font-family: Menlo;
font-size: 11px;">To override the suitability test define:
refinement.input.xray_data.r_free_flags.disable_suitability_test=True</span></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;"><br>
</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">I checked my new mtz file, it dose
contain a column labeled as FreeRflag</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;"><br>
</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">Why there is an error message? How
to solve it?</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;"><br>
</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">Thank you so much!!</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;"><br>
</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">Best wishes!</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;"><br>
</span></font></div>
<div style="margin: 0px;"><font face="Menlo"><span
style="font-size: 14px;">yamei </span></font></div>
<div><br>
</div>
<div>
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<div style="margin: 0px; font-size: 10.5px; color: rgb(47,
42, 43);">************************************************</div>
<div style="margin: 0px; font-size: 10.5px; color: rgb(47,
42, 43);"><br>
</div>
<div style="margin: 0px; font-size: 10.5px; color: rgb(47,
42, 43);">Yamei Yu</div>
<div style="margin: 0px; font-size: 10.5px; color: rgb(47,
42, 43);">State Key Laboratory of Biotherapy／Collaborative
Innovation </div>
<div style="margin: 0px; font-size: 10.5px; color: rgb(47,
42, 43);">Center of Biotherapy, </div>
</div>
<div style="font-family: Helvetica; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; margin: 0px; font-size:
10.5px; color: rgb(47, 42, 43);">
<div style="margin: 0px; font-size: 10.5px;">West China <span
style="font-size: 10.5px;">Hospital, </span></div>
<div style="margin: 0px; font-size: 10.5px;"><span
style="font-size: 10.5px;">Sichuan University,</span><span
style="font-size: 10.5px;">Chengdu,610041, P.R.</span><span
style="font-size: 10.5px;">China</span></div>
<div style="margin: 0px; font-size: 10.5px;">Tel:
15882013485</div>
<div style="margin: 0px; font-size: 10.5px;">Email: <a
moz-do-not-send="true" href="mailto:ymyuxtal@gmail.com">ymyuxtal@gmail.com</a></div>
<div style="margin: 0px; font-size: 10.5px;"> <a
moz-do-not-send="true" href="mailto:ymyuxtal@163.com">ymyuxtal@163.com</a></div>
<div style="margin: 0px; font-size: 10.5px;"> <a
moz-do-not-send="true" href="mailto:yamei_yu@scu.edu.cn">yamei_yu@scu.edu.cn</a></div>
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