<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@SimSun";
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Palatino;
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:"Courier New";}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:172692257;
mso-list-type:hybrid;
mso-list-template-ids:-603163450 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><a name="_MailEndCompose"><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>Hi </span></a><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>J�rgen, Kelly and Nat,<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>I tried XDS and MosFilm, they simply cannot index the data. <o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>I reprocessed the data yesterday with HKL2000 starting from �frame #30 (splitting 1-29, 30-360), I did get it indexed to I4 and refined to very nice x/y chi^2 and covering most spots, I then used the index/refinement numbers for the whole data set. it seems that other spots were from a “nicely” positioned secondary crystal which fooled the program to pick P4 space group.<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>I scaled the data as I4 and I422 to see which one is better. The I4 data set, ~95% complete overall, 9.2% R-sym. Xtriage suggested it should have higher symmetry I422 or twin (-k, -h, -l, almost 50%). MR sent well and best SG is I4, 2 mol/ASU, r� and r-free went to about 27% and 32%, but if I used the twin-law in phenix.refine and ask phenix to generate r-free-flags with twinning in mind, the numbers went to ~22%� and 27%. �<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>Shell Lower Upper Average����� Average���� Norm. Linear Square<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'> limit��� Angstrom������ I�� error�� stat. Chi**2� R-fac� R-fac<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>����� 50.00�� 7.32�� 440.7���� 8.8���� 5.1� 1.481� 0.027� 0.030<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 7.32�� 5.81�� 167.2���� 4.2���� 3.2� 1.868� 0.045� 0.048<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 5.81�� 5.08�� 196.3���� 5.1���� 3.9� 2.130� 0.053� 0.058<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 5.08�� 4.62�� 243.1���� 6.2���� 4.7� 2.264� 0.056� 0.061<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.62�� 4.29�� 236.7���� 6.4���� 4.9� 2.057� 0.055� 0.055<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.29�� 4.03�� 167.6���� 5.6���� 4.7� 1.819� 0.067� 0.066<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.03�� 3.83�� 139.5���� 5.6���� 5.0� 1.740� 0.083� 0.075<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.83�� 3.66�� 110.2���� 5.5���� 5.1� 1.645� 0.102� 0.091<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.66�� 3.52��� 92.5���� 5.6���� 5.3� 1.459� 0.117� 0.101<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.52�� 3.40��� 76.5���� 5.7���� 5.4� 1.372� 0.143� 0.124<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.40�� 3.30��� 59.3���� 5.7���� 5.5� 1.278� 0.179� 0.146<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.30�� 3.20��� 47.3���� 5.7���� 5.6� 1.161� 0.212� 0.179<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.20�� 3.12��� 40.7���� 5.8���� 5.7� 1.103� 0.241� 0.201<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.12�� 3.04��� 31.6���� 5.8���� 5.8� 1.057� 0.298� 0.254<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.04�� 2.97��� 28.9���� 5.9���� 5.9� 1.031� 0.331� 0.271<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.97�� 2.91��� 22.6���� 5.9���� 5.9� 0.985� 0.400� 0.340<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.91�� 2.85��� 19.0���� 6.0���� 6.0� 0.991� 0.484� 0.405<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.85�� 2.80��� 17.1���� 6.1���� 6.1� 0.957� 0.518� 0.437<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.80�� 2.75��� 14.6���� 6.2���� 6.2� 0.908� 0.577� 0.485<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.75�� 2.70��� 13.0���� 6.4���� 6.3� 0.931� 0.645� 0.550<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Courier New"'>� All reflections��� 112.9���� 5.9���� 5.3� 1.455� 0.092� 0.066</span><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>The I422 data (below), 1 mol/ASU, r and r-free were </span><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>about 27% and 32%.</span><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>Shell Lower Upper Average����� Average���� Norm. Linear Square<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'> limit��� Angstrom������ I�� error�� stat. Chi**2� R-fac� R-fac<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>����� 50.00�� 7.32�� 430.0���� 8.4���� 5.0� 1.344� 0.025� 0.028<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 7.32�� 5.81�� 163.4���� 4.0���� 3.0� 1.489� 0.040� 0.042<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 5.81�� 5.08�� 192.4���� 4.8���� 3.6� 1.694� 0.046� 0.052<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 5.08�� 4.62�� 231.6���� 5.6���� 4.3� 1.790� 0.049� 0.053<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.62�� 4.29�� 227.8���� 5.8���� 4.5� 1.534� 0.045� 0.043<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.29�� 4.03�� 161.3���� 5.0���� 4.2� 1.401� 0.055� 0.052<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 4.03�� 3.83�� 135.3���� 5.0���� 4.4� 1.367� 0.066� 0.059<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.83�� 3.66�� 106.2���� 4.9���� 4.4� 1.302� 0.082� 0.071<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.66�� 3.52��� 88.1���� 4.8���� 4.5� 1.253� 0.097� 0.082<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.52�� 3.40��� 75.0���� 4.9���� 4.6� 1.193� 0.113� 0.096<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.40�� 3.30��� 56.7���� 4.8���� 4.6� 1.121� 0.144� 0.115<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.30�� 3.20��� 44.8���� 4.8���� 4.7� 1.061� 0.172� 0.141<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.20�� 3.12��� 38.0���� 4.8���� 4.7� 1.011� 0.203� 0.166<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.12�� 3.04��� 29.1���� 4.7���� 4.7� 1.029� 0.253� 0.209<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 3.04�� 2.97��� 27.7���� 4.8���� 4.8� 0.985� 0.261� 0.209<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.97�� 2.91��� 21.4���� 4.9���� 4.8� 0.917� 0.320� 0.266<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.91�� 2.85��� 18.3���� 4.9���� 4.8� 0.949� 0.380� 0.316<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.85�� 2.80��� 16.1���� 4.9���� 4.9� 0.955� 0.431� 0.358<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.80�� 2.75��� 14.2���� 5.0���� 5.0� 0.940� 0.483� 0.399<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;font-family:"Courier New"'>������ 2.75�� 2.70��� 12.6���� 5.2���� 5.2� 0.886� 0.536� 0.462<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Courier New"'>� All reflections��� 110.9���� 5.1���� 4.5� 1.236� 0.076� 0.054</span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>So my questions are:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>Is it really twinned since including twin-law in refinment gave much better numbers?<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>When refining with twin-law, Are the maps by phenix.refine output already “corrected” mtz/map?</span><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>If I use </span><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>xray_data.r_free_flags.generate=True, can I write the data mtz out with the generated r-free-flags so that each round of refinement uses the same CV set?<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.25in'><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>Thnaks,<o:p></o:p></span></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Tongqing<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Tongqing Zhou, Ph.D.<o:p></o:p></span></b></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Staff Scientist<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Structural Biology Section<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Vaccine Research Center, NIAID/NIH<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Building 40, Room 4609B<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>40 Convent Drive, MSC3027<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Bethesda, MD 20892<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>(301) 594-8710 (Tel)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>(301) 793-0794 (Cell)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>(301) 480-2658 (Fax)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#A6A6A6'>******************************************************************************<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#A6A6A6'>The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#A6A6A6'>******************************************************************</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#A6A6A6'><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Bosch, Juergen [mailto:jubosch@jhsph.edu] <br><b>Sent:</b> Monday, May 07, 2012 1:34 PM<br><b>To:</b> PHENIX user mailing list<br><b>Subject:</b> Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinning?<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Why don't you index over the whole dataset (XDS) ?<o:p></o:p></p><div><p class=MsoNormal>Or at least over a couple of images (Mosflm)<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>J�rgen<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On May 7, 2012, at 12:50 PM, Kelly Daughtry wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>I agree.<br><br>The fact that two "crystals forms" appear, with related unit cells:<br>P422 data:<br> unit_cell = 191.6999969 191.6999969 311.0539856 90 90 90<br> space_group = "P 4 2 2"<br>I422 data:<br>unit_cell = 191.783 191.783 103.775 90 90 90<br> space_group = "I 4 2 2"<br><br>indicated to me you have mis-indexed the P422 data. It is likely I422.<br>Kelly<br>*******************************************************<br>Kelly Daughtry, Ph.D.<br>Post-Doctoral Fellow, Raetz Lab<br>Biochemistry Department<br>Duke University<br>Alex H. Sands, Jr. Building<br>303 Research Drive<br>RM 250<br>Durham, NC 27710<br>P: 919-684-5178<br>*******************************************************<br><br><br>On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>> wrote:<br><br><o:p></o:p></p><p class=MsoNormal>On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry <<a href="mailto:kddaught@bu.edu">kddaught@bu.edu</a>> wrote:<o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Looking at the P422 data, it look like you have pseudo translational symmetry.<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Did you try processing this data as I422?<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><o:p> </o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>From the P422_xtriage.log:<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><o:p> </o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>The full list of Patterson peaks is:<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><o:p> </o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal> x y z height p-value(height)<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>( 0.500, 0.500, 0.165 ) : 78.635 (6.634e-07)<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>( 0.000, 0.000, 0.330 ) : 56.292 (2.795e-05)<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>( 0.500, 0.500, 0.497 ) : 30.920 (1.207e-03)<o:p></o:p></p></blockquote></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><o:p> </o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>One word of caution: an exceptionally high off-origin peak can mean<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>that the unit cell was measured too large, and you've integrated extra<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>reflections that are really non-existent. (I'm not sure what the<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>threshold for this is, but 80% seems pretty large.) Splitting and<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>various indexing artifacts can sometimes lead to this. I'd recommend<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>running labelit.index on the images and seeing what it thinks the<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>lattice should be.<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><o:p> </o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>-Nat<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>_______________________________________________<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>phenixbb mailing list<o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></p></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></p></blockquote><p class=MsoNormal>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span class=apple-style-span><span style='font-size:13.5pt;font-family:"Palatino","serif";color:black'>......................</span></span><span style='font-size:13.5pt;font-family:"Palatino","serif";color:black'><br><span class=apple-style-span>J�rgen Bosch</span><br><span class=apple-style-span>Johns Hopkins University</span><br><span class=apple-style-span>Bloomberg School of Public Health</span><br><span class=apple-style-span>Department of Biochemistry & Molecular Biology</span><br><span class=apple-style-span>Johns Hopkins Malaria Research Institute</span><br><span class=apple-style-span>615 North Wolfe Street, W8708</span><br><span class=apple-style-span>Baltimore, MD 21205</span><br><span class=apple-style-span>Office: +1-410-614-4742</span><br><span class=apple-style-span>Lab: +1-410-614-4894</span><br><span class=apple-style-span>Fax: +1-410-955-2926</span><br><span class=apple-style-span><a href="http://web.mac.com/bosch_lab/">http://web.mac.com/bosch_lab/</a></span><br><br><br><br><br></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>