<div dir="ltr">Hi Ryan, <div><br></div><div>Thank you very much! Below are the summary of my pointless log after "quick scale" from Imosflm (this time I force imosflm to choose P1 in the integration and scale but pointless chose P31):</div><div><br></div><div> <span style="color:rgb(0,0,0);font-family:courier">$TEXT:Result: $$ $$</span></div>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Summary data for Project: New Crystal: New Dataset: New</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> Overall InnerShell OuterShell</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Low resolution limit 82.13 82.13 2.49</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">High resolution limit 2.40 8.98 2.40</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rmerge (within I+/I-) 0.075 0.033 0.851</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rmerge (all I+ and I-) 0.086 0.048 0.919</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rmeas (within I+/I-) 0.089 0.039 1.007</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rmeas (all I+ & I-) 0.093 0.052 0.996</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rpim (within I+/I-) 0.047 0.021 0.534</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rpim (all I+ & I-) 0.035 0.021 0.380</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Rmerge in top intensity bin 0.031 - - </span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Total number of observations 214291 4072 22139</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Total number unique 31247 617 3299</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Mean((I)/sd(I)) 14.4 29.4 2.9</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Mn(I) half-set correlation CC(1/2) 0.998 0.995 0.785</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Completeness 100.0 99.9 99.8</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Multiplicity 6.9 6.6 6.7</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier"><b><font color="#ff0000">Anomalous completeness 99.7 98.1 98.8</font></b></span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier"><b><font color="#ff0000">Anomalous multiplicity 3.4 3.4 3.3</font></b></span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier"><b><font color="#ff0000">DelAnom correlation between half-sets 0.303 0.473 0.046</font></b></span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier"><b><font color="#ff0000">Mid-Slope of Anom Normal Probability 1.161 - - </font></b></span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier"><b><font color="#ff0000"><br></font></b></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier"><b><font color="#ff0000">Estimate of maximum resolution for significant anomalous signal = 3.97A, from CCanom > 0.15</font></b></span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Estimates of resolution limits: overall</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from Mn(I/sd) > 1.50: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from Mn(I/sd) > 2.00: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Estimates of resolution limits in reciprocal lattice directions:</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> Along h k plane</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from Mn(I/sd) > 1.50: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> Along l axis</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from half-dataset correlation CC(1/2) > 0.30: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"> from Mn(I/sd) > 1.50: limit = 2.40A == maximum resolution</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Anisotropic deltaB (i.e. range of principal components), A^2: 12.33</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Average unit cell: 65.87 65.87 164.25 90.00 90.00 120.00 </span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Space group: P 31</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Average mosaicity: 0.58</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Minimum and maximum SD correction factors: Fulls 1.07 104.68 Partials 1.18 134.50</span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">Anomalous flag switched ON in input, strong anomalous signal found</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">$$ </span></pre>
<pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">==============================================================</span></pre><pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)"><br></span></pre><pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">I do not know if this data set with such anomalous completeness and multiplicity is enough for me to get phase information to </span></pre><pre style="margin-top:0px;margin-bottom:0px"><span style="font-family:courier;color:rgb(0,0,0)">locate the Iodine, I do not have native dataset, and only have iodine soaking dataset.</span></pre>
<pre style="margin-top:0px;margin-bottom:0px;font-family:courier;color:rgb(0,0,0)"><br></pre></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 12, 2016 at 11:53 AM, rspencer <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="#0563C1" vlink="#954F72"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi Alex,<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">You need to look at you anomalous signal in the aimless.log output to see if there was a detectable anomalous signal. You can also force iMosflm to treat the dataset as having an anomalous signal so that it won’t merge your intensities.<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">Soaking does not guarantee that you will have an anomalous signal in your crystal and you may need to do a multiple crystals with increasing soak time to get an anomalous signal. You can easily do this by soaking the crystal and checking a few frames on your in-house source. Process the frames and see if an anomalous signal is detected.<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">Good luck!<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"><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>Alex Lee<br><b>Sent:</b> Tuesday, April 12, 2016 11:09 AM<br><b>To:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><b>Subject:</b> [phenixbb] Phenix Xtriage label error<u></u><u></u></span></p><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">Dear Phenixbb members,<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The protein crystal was soaked in potassium iodine before collecting data using in-house beam (1.54A wavelength). As I expected some anomalous signal from the iodine ion from the crystal, after I use Imosflm to index, integrate and scale the data (space group P3). I got four output .mtz files: pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only unmerged mtz data is pointless_XXX.mtz, the other three mtz files are merged. <u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to check my mtz data for anomalous completeness, I thought in this step my mtz should be unmerged type to see the anomalous signal, so I chose "pointless_xxx.mtz" as Xtriage input, but for the data labels in the Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz label. I decide to leave this choice blank by choosing data labels"---". After I click "run", Xtriage gave an error "please select labels for input data". <u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Any input on this issue? <u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Thanks in advance.<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div></div></div></div></div></div></blockquote></div><br></div>