<div dir="ltr">Thanks a lot, Dr .Tanner. I will try the suggestion. Currently, I tried running xds_ASCII.HKL on pointless followed by truncate. Seems like mtz is now all good. But I am wondering if this is the right way to go about it?<div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 12, 2022 at 8:33 PM Tanner, John J. <<a href="mailto:TannerJJ@missouri.edu">TannerJJ@missouri.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt">This is a common problem. I use ccp4i CAD to remove all the columns from the .mtz file except for F, SIGF, and FreeR_flag, and then use this new .mtz file in refinement before depositing. For the next structure,
remember to do this in the early stages. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">--<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">John J. Tanner </span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Professor of Biochemistry and Chemistry</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Associate Chair of Biochemistry</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Department of Biochemistry</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">University of Missouri<br>
117 Schweitzer Hall</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">503 S College Avenue<br>
Columbia, MO 65211<br>
Phone: 573-884-1280</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black"><a href="mailto:tannerjj@missouri.edu" title="mailto:tannerjj@missouri.edu" target="_blank"><span style="color:rgb(5,99,193)">Email: tannerjj@missouri.edu</span></a><br>
<a href="https://cafnrfaculty.missouri.edu/tannerlab/" title="https://cafnrfaculty.missouri.edu/tannerlab/" target="_blank"><span style="color:rgb(5,99,193)">https://cafnrfaculty.missouri.edu/tannerlab/</span></a></span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;font-family:Helvetica;color:black;background:white">Office: Schlundt Annex 203A</span><span style="font-size:11pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black"><a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>> on behalf of Viney Singh <<a href="mailto:vineysingh22@gmail.com" target="_blank">vineysingh22@gmail.com</a>><br>
<b>Date: </b>Wednesday, January 12, 2022 at 6:52 AM<br>
<b>To: </b><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a> <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
<b>Subject: </b>[phenixbb] regarding number of unique reflections<u></u><u></u></span></p>
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<p class="MsoNormal" style="line-height:12pt;background:rgb(255,199,206)"><b><span style="color:rgb(156,0,6)">WARNING:</span></b><span style="color:black"> This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized
access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Dear all, <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">First of all sorry for the novice question.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">I <u>processed</u> one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True. <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">The number of unique reflections I got:
<b>17,000</b><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Now, when I am trying to<u> refine
</u>the structure in Phenix, the structure is being refined against <b>32,300</b> reflections with
<b>3230</b> reflections for Rfree calculation. Looks like refinement is treating Friedel's pair as two different reflections. <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">When I am trying to upload PDB on rcsb, on the refinement tab, the number of reflections used for refinement and Rfree calculations are shown as 32,300 and 3220 respectively, while in the validation report,
no. of reflections used for Rfree calculation are shown as <b>1700</b>.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">I would really appreciate if someone can guide me to resolve this discrepancy. <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Thanks in advance.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Viney<u></u><u></u></span></p>
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