<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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