<div dir="ltr"><div>Hi Alex,</div><div><br></div>HKL2000 removes the systematic absences according to the p2221 spacegroup. <div>Xtriage doesn't see them and can't do anything with them. For this reason, the Wilson statistics likelihood score used to determine the spacegroup for P222 and P2221 are exactly the same. </div><div><br></div><div>Peter<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 23 January 2016 at 09:11, Alex Lee <span dir="ltr"><<a href="mailto:alexlee198609@gmail.com" target="_blank">alexlee198609@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear All,</div><div><br></div><div>I scaled a dataset of SG P2221 in HKL2000 and got systematic absence results as below, it seems clearly HKL2000 showed the data had systematic absence violations, but when I used the .sca file from HKL2000 as input in Xtriage, the result did not show any systematic violations. Which result should I rely on?</div><div><br></div><div>HKL200 Results:</div><div><div> Summary of reflections intensities and R-factors by shells</div><div> R linear = SUM ( ABS(I - <I>)) / SUM (I)</div><div> R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2)</div><div> Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) )</div><div> In all sums single measurements are excluded</div><div><br></div><div> Shell Lower Upper Average Average Norm. Linear Square</div><div> limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC*</div><div> 50.00 5.60 2819.0 103.7 44.8 0.607 0.033 0.040 0.037 0.017 0.998 0.999</div><div> 5.60 4.45 1801.5 63.8 28.1 0.914 0.043 0.050 0.048 0.022 0.997 0.999</div><div> 4.45 3.88 1435.3 52.6 25.5 0.980 0.048 0.051 0.054 0.024 0.997 0.999</div><div> 3.88 3.53 738.7 31.8 20.5 1.117 0.068 0.067 0.075 0.032 0.996 0.999</div><div> 3.53 3.28 489.7 26.5 20.1 1.134 0.092 0.080 0.102 0.043 0.996 0.999</div><div> 3.28 3.08 236.3 19.8 17.4 0.975 0.147 0.108 0.162 0.069 0.993 0.998</div><div> 3.08 2.93 93.4 16.4 16.0 0.850 0.296 0.277 0.327 0.138 0.947 0.986</div><div> 2.93 2.80 62.9 16.3 16.0 0.737 0.422 0.384 0.467 0.197 0.921 0.979</div><div> 2.80 2.69 42.6 16.7 16.5 0.677 0.622 0.515 0.688 0.291 0.879 0.967</div><div> 2.69 2.60 29.3 20.0 19.9 0.680 0.924 0.842 0.000 0.440 0.659 0.891</div><div> All reflections 798.1 37.4 22.6 0.873 0.064 0.050 0.068 0.031</div><div><br></div><div> Intensities of systematic absences</div><div> h k l Intensity Sigma I/Sigma</div><div><br></div><div> 0 0 3 -0.4 1.3 -0.3</div><div> 0 0 5 10.4 3.0 3.5</div><div> 0 0 7 11.4 3.9 2.9</div><div> 0 0 9 8.7 4.3 2.0</div><div> 0 0 11 18.6 6.4 2.9</div><div> 0 0 13 182.9 17.1 10.7</div><div> 0 0 15 3.0 7.8 0.4</div><div> 0 0 17 11.9 9.2 1.3</div><div> 0 0 19 30.0 14.3 2.1</div><div> 0 0 21 7.4 11.1 0.7</div><div> 0 0 23 54.2 15.6 3.5</div><div> 0 0 25 43.1 16.1 2.7</div><div> 0 0 27 12.5 18.9 0.7</div><div> 0 0 29 -16.6 20.9 -0.8</div><div> 0 0 31 31.0 25.4 1.2</div><div> 0 0 33 3.4 29.2 0.1</div><div> 0 0 35 -24.2 32.0 -0.8</div><div> 0 0 37 50.9 42.5 1.2</div><div> 0 0 39 -53.3 66.4 -0.8</div><div> 0 0 41 65.8 50.6 1.3</div><div> 0 0 43 -24.3 46.8 -0.5</div><div> 0 0 45 -6.1 48.3 -0.1</div><div> 0 0 47 -14.8 45.8 -0.3</div><div> 0 0 49 1.1 53.5 0.0</div><div> 0 0 51 -7.9 64.2 -0.1</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>Phenix Xtriage Results:</div><div><br></div><div> ----------Space group identification----------</div><div><br></div><div>Analyses of the absences table indicates a number of likely space group</div><div>candidates, which are listed below. For each space group, the number of</div><div>systematic absence violations are listed under the '+++' column. The number of</div><div>non-absence violations (weak reflections) are listed under '---'. The last</div><div>column is a likelihood based score for the particular space group. Note that</div><div>enantiomorphic spacegroups will have equal scores. Also, if absences were</div><div>removed while processing the data, they will be regarded as missing</div><div>information, rather then as enforcing that absence in the space group choices.</div><div><br></div><div> -------------------------------------------------------------------------------------</div><div> | space group | # absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score |</div><div> -------------------------------------------------------------------------------------</div><div> | P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 |</div><div> | P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 |</div><div> | P 2 21 2 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 |</div><div> | P 2 21 21 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 |</div><div> | P 21 2 2 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 |</div><div> | P 21 2 21 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 |</div><div> | P 21 21 2 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 |</div><div> | P 21 21 21 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 |</div><div> -------------------------------------------------------------------------------------</div><div><br></div><div> ----------List of individual systematic absences----------</div><div><br></div><div> Note: this analysis uses the original input data rather than the filtered data</div><div> used for twinning detection; therefore, the results shown here may include</div><div> more reflections than shown above.</div><div><br></div><div>P 2 2 2: no systematic absences possible</div><div>P 2 2 21 (input space group): no absences found</div><div>P 21 2 2</div><div> ( 5, 0, 0): i/sigi = 21.0</div><div> ( 7, 0, 0): i/sigi = 4.8</div><div> ( 9, 0, 0): i/sigi = 14.3</div><div> ( 11, 0, 0): i/sigi = 15.2</div><div> ( 13, 0, 0): i/sigi = 18.3</div><div> ( 15, 0, 0): i/sigi = 12.7</div><div> ( 17, 0, 0): i/sigi = 4.1</div><div>P 2 21 2</div><div> ( 0, 3, 0): i/sigi = 21.3</div><div> ( 0, 5, 0): i/sigi = 21.4</div><div> ( 0, 7, 0): i/sigi = 20.7</div><div> ( 0, 9, 0): i/sigi = 21.4</div><div> ( 0, 11, 0): i/sigi = 20.7</div><div> ( 0, 13, 0): i/sigi = 14.5</div><div> ( 0, 17, 0): i/sigi = 10.4</div><div> ( 0, 21, 0): i/sigi = 14.4</div><div> ( 0, 23, 0): i/sigi = 0.8</div><div> ( 0, 25, 0): i/sigi = 2.3</div><div> ( 0, 27, 0): i/sigi = 2.0</div><div>P 21 21 2</div><div> ( 0, 3, 0): i/sigi = 21.3</div><div> ( 0, 5, 0): i/sigi = 21.4</div><div> ( 0, 7, 0): i/sigi = 20.7</div><div> ( 0, 9, 0): i/sigi = 21.4</div><div> ( 0, 11, 0): i/sigi = 20.7</div><div> ( 0, 13, 0): i/sigi = 14.5</div><div> ( 0, 17, 0): i/sigi = 10.4</div><div> ( 0, 21, 0): i/sigi = 14.4</div><div> ( 0, 23, 0): i/sigi = 0.8</div><div> ( 0, 25, 0): i/sigi = 2.3</div><div> ( 0, 27, 0): i/sigi = 2.0</div><div> ( 5, 0, 0): i/sigi = 21.0</div><div> ( 7, 0, 0): i/sigi = 4.8</div><div> ( 9, 0, 0): i/sigi = 14.3</div><div> ( 11, 0, 0): i/sigi = 15.2</div><div> ( 13, 0, 0): i/sigi = 18.3</div><div> ( 15, 0, 0): i/sigi = 12.7</div><div> ( 17, 0, 0): i/sigi = 4.1</div><div>P 2 21 21</div><div> ( 0, 3, 0): i/sigi = 21.3</div><div> ( 0, 5, 0): i/sigi = 21.4</div><div> ( 0, 7, 0): i/sigi = 20.7</div><div> ( 0, 9, 0): i/sigi = 21.4</div><div> ( 0, 11, 0): i/sigi = 20.7</div><div> ( 0, 13, 0): i/sigi = 14.5</div><div> ( 0, 17, 0): i/sigi = 10.4</div><div> ( 0, 21, 0): i/sigi = 14.4</div><div> ( 0, 23, 0): i/sigi = 0.8</div><div> ( 0, 25, 0): i/sigi = 2.3</div><div> ( 0, 27, 0): i/sigi = 2.0</div><div>P 21 2 21</div><div> ( 5, 0, 0): i/sigi = 21.0</div><div> ( 7, 0, 0): i/sigi = 4.8</div><div> ( 9, 0, 0): i/sigi = 14.3</div><div> ( 11, 0, 0): i/sigi = 15.2</div><div> ( 13, 0, 0): i/sigi = 18.3</div><div> ( 15, 0, 0): i/sigi = 12.7</div><div> ( 17, 0, 0): i/sigi = 4.1</div><div>P 21 21 21</div><div> ( 0, 3, 0): i/sigi = 21.3</div><div> ( 0, 5, 0): i/sigi = 21.4</div><div> ( 0, 7, 0): i/sigi = 20.7</div><div> ( 0, 9, 0): i/sigi = 21.4</div><div> ( 0, 11, 0): i/sigi = 20.7</div><div> ( 0, 13, 0): i/sigi = 14.5</div><div> ( 0, 17, 0): i/sigi = 10.4</div><div> ( 0, 21, 0): i/sigi = 14.4</div><div> ( 0, 23, 0): i/sigi = 0.8</div><div> ( 0, 25, 0): i/sigi = 2.3</div><div> ( 0, 27, 0): i/sigi = 2.0</div><div> ( 5, 0, 0): i/sigi = 21.0</div><div> ( 7, 0, 0): i/sigi = 4.8</div><div> ( 9, 0, 0): i/sigi = 14.3</div><div> ( 11, 0, 0): i/sigi = 15.2</div><div> ( 13, 0, 0): i/sigi = 18.3</div><div> ( 15, 0, 0): i/sigi = 12.7</div><div> ( 17, 0, 0): i/sigi = 4.1</div><div><br></div><div>Thanks ahead</div></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>-----------------------------------------------------------------<br>P.H. Zwart<br>Staff Scientist<br>Berkeley Center for Structural Biology, Science lead<br>Lawrence Berkeley National Laboratories<br>1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>SASTBX: <a href="http://sastbx.als.lbl.gov" target="_blank">http://sastbx.als.lbl.gov</a></div><div>BCSB: <a href="http://bcsb.als.lbl.gov" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div>PHENIX: <a href="http://www.phenix-online.org" target="_blank">http://www.phenix-online.org</a></div><div>CAMERA: <a href="http://camera.lbl.gov/" target="_blank">http://camera.lbl.gov/</a></div><div>-----------------------------------------------------------------</div></div></div></div></div>
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