<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Why does .CIF file output by phenix.refine contain all of the -h -k -l reflections. The Bijvoet reflections are already contained in the _refln.pdbx_F_minus column of the +h +k +l reflections. When OneDep at PDB reads in these files, it finds ‘?’ in about half of the reflections, and assigns them a status of ‘x':<div class=""><br class=""></div><div class=""><span style="color: rgb(205, 10, 10); font-family: monospace; font-size: 13.2px; font-variant-ligatures: normal; font-weight: 700; orphans: 2; white-space: pre-line; widows: 2; background-color: rgb(255, 255, 255); text-decoration-thickness: initial;" class="">Warning: (data block=1): 36739 reflections have status assigned as '?' (changed to 'x')
Warning: (data block=1): 36739 reflections have wrong status. Not in list(o,f,x,-,<,h,l)</span></div><div class=""><div style="orphans: 2; widows: 2;" class=""><font color="#cd0a0a" face="monospace" size="2" class=""><span style="caret-color: rgb(205, 10, 10); white-space: pre-line; background-color: rgb(255, 255, 255);" class=""><b class=""><br class=""></b></span></font></div><div style="orphans: 2; widows: 2;" class="">Is this the correct behavior? My space group is 19.</div><div style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class="">Thanks,</div><div style="orphans: 2; widows: 2;" class="">Mark</div><div class=""><br class=""><div class="">
<meta charset="UTF-8" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div>_____________________<br class=""><b class=""><font color="#011993" class="">Mark A. Saper, Ph.D.</font></b><br class=""><span style="font-style: normal; font-size: 12px;" class="">Associate Professor Emeritus of Biological Chemistry<br class="">University of Michigan Medical School<br class=""><a href="mailto:saper@umich.edu" class="">saper@umich.edu</a> | +1 734 276 6505</span><br class=""></div></div>
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