<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><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><div apple-content-edited="true"><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;"><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 href="mailto:ymyuxtal@gmail.com">ymyuxtal@gmail.com</a></div><div style="margin: 0px; font-size: 10.5px;"> <a href="mailto:ymyuxtal@163.com">ymyuxtal@163.com</a></div><div style="margin: 0px; font-size: 10.5px;"> <a href="mailto:yamei_yu@scu.edu.cn">yamei_yu@scu.edu.cn</a></div></div>
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