<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body >The question then becomes how do you know the bromine is in the crystal? Is it covalent on the protein? Is it covalent on the ligand? How do you know if the ligand is in the structure?<div><br></div><div>We have seen rapid crystal degredation with Br at its edge. Do you see the resolution significantly degrade after a few frames?</div><div><br></div><div>I don't think it's a processing issue with xds or with phenix.</div><div><br></div><div>Ryan</div><br><br><br>-------- Original message --------<br>From: CPMAS Chen <cpmasmit@gmail.com> <br>Date: 07/10/2014 9:52 AM (GMT-08:00) <br>To: Ryan Spencer <rspencer@uci.edu> <br>Cc: Francis Reyes <Francis.Reyes@colorado.edu>,phenixbb@phenix-online.org <br>Subject: Re: [phenixbb] Anomalous or not? <br> <br><br><div dir="ltr">Well, let me make this clear.<div><br></div><div>1. I am using Br anomalous signal to identify the potentially bound ligand.</div><div>2. I do shoot the crystals at 0.92A.</div><div>3. the different crystals have different resolution, but anomalous signal was weak as reported by autoxds.</div>
<div><br></div><div>Charles</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <span dir="ltr"><<a href="mailto:rspencer@uci.edu" target="_blank">rspencer@uci.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or are the crystals sensitive? If you were limited to the single wavelength beam which is around 1A you’re dealing with a really low f” of 0.5322. There have been crystals solved with Sulfur using an in-house Cu sources (takes a lot of merged sets and anomalous is stronger at certain crystal angles) which gives about the same anomalous scattering as Br. Is the bromine covalent or is it soaked ion?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Alternatives – soak with potassium iodide and get a dataset from an in-house source (iodine f” 6.6 at 1.54), or at least the anomalous locations. You may get a partial model to use for replacement at that point.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Did each processed dataset have the same level of anomalous signal when processed individually?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ryan<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] <b>On Behalf Of </b>CPMAS Chen<br>
<b>Sent:</b> Thursday, July 10, 2014 8:55 AM<br><b>To:</b> Francis Reyes<br><b>Cc:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><b>Subject:</b> Re: [phenixbb] Anomalous or not?<u></u><u></u></span></p>
<div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">Francis,<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">My anomalous plot for Br is more like your Cobalt 1 site less redundancy.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Ryan,<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">As my Br anomalous signals are weak, I merged signals from multiple crystals.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Meanwhile I am looking into the detail about the autoxds processing as suggested by Tim. <u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></p></div><div><p class="MsoNormal">Thanks,<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p><div><p class="MsoNormal">On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <<a href="mailto:Francis.Reyes@colorado.edu" target="_blank">Francis.Reyes@colorado.edu</a>> wrote:<u></u><u></u></p>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in"><p class="MsoNormal">In addition to Tim's comments above, using loggraph to see the anomalous CC plot from scala is a good qualitative indicator of whether you have anomalous signal..<br>
<br><br>Some data points for what reasonable plots (and their corresponding XDS SigANO's) look like: <a href="https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf" target="_blank">https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf</a><br>
<span style="color:#888888"><br><br><span>F</span></span><u></u><u></u></p><div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>On Jul 10, 2014, at 9:03 AM, CPMAS Chen <<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>> wrote:<br>
<br>><br>> Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i.<br>><u></u><u></u></p></div></div></blockquote>
</div><p class="MsoNormal"><br><br clear="all"><u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">-- <u></u><u></u></p><p>***************************************************<u></u><u></u></p>
<p>Charles Chen<u></u><u></u></p><p>Research Associate<u></u><u></u></p><p>University of Pittsburgh School of Medicine<u></u><u></u></p><p>Department of Anesthesiology<u></u><u></u></p><p>******************************************************<u></u><u></u></p>
</div></div></div></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>
<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p>
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