Ignore:
Timestamp:
Mar 17, 2015 2:28:32 PM (9 years ago)
Author:
vondreele
Message:

update sucrose charge flipping

File:
1 edited

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  • Tutorials/CFsucrose/Charge Flipping - sucrose.htm

    r1717 r1730  
    2424  <o:Author>Von Dreele</o:Author>
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    26   <o:Revision>2</o:Revision>
    27   <o:TotalTime>1435</o:TotalTime>
     26  <o:Revision>3</o:Revision>
     27  <o:TotalTime>1520</o:TotalTime>
    2828  <o:Created>2015-03-16T21:09:00Z</o:Created>
    29   <o:LastSaved>2015-03-16T21:09:00Z</o:LastSaved>
     29  <o:LastSaved>2015-03-17T19:23:00Z</o:LastSaved>
    3030  <o:Pages>1</o:Pages>
    31   <o:Words>3473</o:Words>
    32   <o:Characters>19801</o:Characters>
     31  <o:Words>3448</o:Words>
     32  <o:Characters>19655</o:Characters>
    3333  <o:Company>Argonne National Laboratory</o:Company>
    34   <o:Lines>165</o:Lines>
     34  <o:Lines>163</o:Lines>
    3535  <o:Paragraphs>46</o:Paragraphs>
    36   <o:CharactersWithSpaces>23228</o:CharactersWithSpaces>
     36  <o:CharactersWithSpaces>23057</o:CharactersWithSpaces>
    3737  <o:Version>15.00</o:Version>
    3838 </o:DocumentProperties>
    … …  
    4646<!--[if gte mso 9]><xml>
    4747 <w:WordDocument>
     48  <w:SpellingState>Clean</w:SpellingState>
     49  <w:GrammarState>Clean</w:GrammarState>
    4850  <w:TrackMoves>false</w:TrackMoves>
    4951  <w:TrackFormatting/>
    … …  
    804806        mso-hansi-font-family:Tahoma;
    805807        mso-bidi-font-family:Tahoma;}
     808span.SpellE
     809        {mso-style-name:"";
     810        mso-spl-e:yes;}
     811span.GramE
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     813        mso-gram-e:yes;}
    806814.MsoChpDefault
    807815        {mso-style-type:export-only;
    … …  
    12571265with particular care. We have given a route that sometimes works.</p>
    12581266
    1259 <p class=MsoNormal>If you have not done so already, <a
    1260 href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a> and open the
    1261 GSAS-II project file (I called it <b style='mso-bidi-font-weight:normal'><span
    1262 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1263 mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b>) you saved from the
    1264 third part of the <a
    1265 href="../../../GSASII/help/Fit%20Peaks.htm#sucrose_peak_fit">peak
    1266 fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
     1267<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
     1268GSAS-II project file (I called it <span class=SpellE><b style='mso-bidi-font-weight:
     1269normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1270minor-latin;mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>)
     1271you saved from the third part of the peak fitting-indexing exercise. If you
     1272didn’t do that exercise, do it now.</p>
    12671273
    12681274<h2>Step 1: Setup for Pawley refinement</h2>
    … …  
    12841290symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
    12851291relatively clear of peaks that makes a good place to end the calculations with
    1286 a reflection set of d<sub>min</sub> ~1Å resolution needed for charge flipping.
    1287 Enter <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1288 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b>
    1289 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1290 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b>
     1292a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
     1293needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
     1294style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1295mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
     1296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
    12911298as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
    12921299mouse cursor on the plot.</p>
    … …  
    13381345mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
    13391346style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1340 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>
    1341 box.</p>
     1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1348class=SpellE>dmin</span></span></b> box.</p>
    13421349
    13431350<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
    … …  
    13651372 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13661373 <o:lock v:ext="edit" aspectratio="t"/>
    1367 </v:shapetype><v:shape id="Picture_x0020_25" o:spid="_x0000_i1064" type="#_x0000_t75"
    1368  style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
     1374</v:shapetype><v:shape id="_x0000_i1064" type="#_x0000_t75" style='width:542.25pt;
     1375 height:375pt;visibility:visible;mso-wrap-style:square'>
    13691376 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
    1370 </v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
    1371 src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1377</v:shape><![endif]--><![if !vml]><img width=723 height=500
     1378src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="_x0000_i1064"><![endif]></span></p>
    13721379
    13731380<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    … …  
    13831390 height:252pt;visibility:visible;mso-wrap-style:square'>
    13841391 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
    1385 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
     1392</v:shape><![endif]--><![if !vml]><img width=346 height=336
    13861393src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
    13871394
    13881395<p class=MsoNormal>Select either choice; the desired data set will be added to
    1389 this phase for analysis. The data tab now shows the new data set; check the <b
    1390 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1391 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    1392 button to see the full information</p>
    1393 
    1394 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1395  id="Picture_x0020_3" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:480pt;
    1396  height:393pt;visibility:visible;mso-wrap-style:square'>
     1396this phase for analysis. The data tab now shows the new data set.</p>
     1397
     1398<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1399 id="_x0000_i1062" type="#_x0000_t75" style='width:359.25pt;height:375pt;
     1400 visibility:visible;mso-wrap-style:square'>
    13971401 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
    1398 </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=524
    1399 src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1402</v:shape><![endif]--><![if !vml]><img width=479 height=500
     1403src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="_x0000_i1062"><![endif]></span></p>
    14001404
    14011405<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    14021406contents. This is the location for all the phase dependent parameters for this
    1403 histogram. Notice that it includes phase fraction, size &amp; mustrain as well
    1404 as preferred orientation, elastic strain and extinction corrections. The
    1405 Babinet correction is intended for protein work where a significant region of
    1406 the structure is disordered solvent. There are buttons for plotting size and
    1407 mustrain surfaces</p>
    1408 
    1409 <p class=MsoNormal>as well as preferred orientation correction curves.</p>
     1407histogram. Notice that it includes phase fraction, size &amp; <span
     1408class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
     1409and extinction corrections. The <span class=SpellE>Babinet</span> correction is
     1410intended for protein work where a significant region of the structure is
     1411disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1412surfaces</p>
     1413
     1414<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
     1415correction curves.</p>
    14101416
    14111417<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    … …  
    14171423makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
    14181424normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1419 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
    1420 should list reflections 0-781. Select and check the refine column using the
    1421 same technique you used for the peak list. </p>
     1425minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
     1426The table should list reflections 0-780. Select and check the refine column
     1427using the same technique you used for the peak list. </p>
    14221428
    14231429<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    14251431 height:225pt;visibility:visible;mso-wrap-style:square'>
    14261432 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
    1427 </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
     1433</v:shape><![endif]--><![if !vml]><img width=500 height=300
    14281434src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
    14291435
    … …  
    14501456style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14511457mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1452 to make sure it has essentially minimized. My refinement completed with Rwp
    1453 ~26.3%; a dialog box appears asking if you wish to load the result. Press <b
    1454 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1455 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1456 To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
    1457 the width and height).</p>
    1458 
    1459 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1460  id="Picture_x0020_5" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:503.25pt;
    1461  height:431.25pt;visibility:visible;mso-wrap-style:square'>
     1458to make sure it has essentially minimized. My refinement completed with <span
     1459class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
     1460the result. Press <b style='mso-bidi-font-weight:normal'><span
     1461style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1462mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
     1463PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
     1464
     1465<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1466 id="Picture_x0020_46" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:525pt;
     1467 height:450pt;visibility:visible;mso-wrap-style:square'>
    14621468 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
    1463 </v:shape><![endif]--><![if !vml]><img border=0 width=671 height=575
    1464 src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1469</v:shape><![endif]--><![if !vml]><img width=700 height=600
     1470src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
    14651471
    14661472<p class=MsoNormal>It is evident from examining the plot that some improvement
    … …  
    14821488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
    14831489style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1484 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&amp;<b
    1485 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1486 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>.
    1487 The go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1488 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
    1489 Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span
    1490 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1491 mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make the <b
    1492 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1493 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer
    1494 radius</span></b> <b style='mso-bidi-font-weight:normal'><span
    1495 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1496 mso-hansi-theme-font:minor-latin'>1000</span></b> if you didn’t do this earlier.
    1497 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1498 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine
    1499 </span></b>until converged; I obtained an improved residual of ~9.05% with a
    1500 much better fit at the high angle part of the pattern but still not fit well
    1501 for the lower part.</p>
     1490mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
     1491class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
     1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1493mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
     1494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1495minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
     1496check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     1498class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
     1499normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1500minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
     1501style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
     1503if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
     1504style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1505mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
     1506I obtained an improved residual of ~9.05% with a much better fit at the high
     1507angle part of the pattern but still not fit well for the lower part.</p>
    15021508
    15031509<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    15051511 height:432.75pt;visibility:visible;mso-wrap-style:square'>
    15061512 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
    1507 </v:shape><![endif]--><![if !vml]><img border=0 width=673 height=577
     1513</v:shape><![endif]--><![if !vml]><img width=673 height=577
    15081514src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    15091515
    … …  
    15251531 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    15261532 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
    1527 </v:shape><![endif]--><![if !vml]><img border=0 width=489 height=263
     1533</v:shape><![endif]--><![if !vml]><img width=489 height=263
    15281534src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
    15291535style='mso-spacerun:yes'> </span></p>
    … …  
    15311537<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
    15321538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1533 mso-hansi-theme-font:minor-latin'>5.0</span></b> for <b style='mso-bidi-font-weight:
    1534 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1535 minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>, <b
    1536 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1539mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
     1540style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
     1542<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15371543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
    1538 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1539 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b>
    1540 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1544for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1545style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1546mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
     1547style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15411548mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
    15421549for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    … …  
    15441551(as appropriate for broad diffuse peaks) and then check all three refine boxes.
    15451552Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1546 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
    1547 pulldown to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1548 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1549 minor-latin'>5</span></b> for the chebyschev part of the background. The window
     1553mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
     1554class=SpellE>coeff</span>.</span></b> <span class=GramE>pulldown</span> to <b
     1555style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1556mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
     1557for the <span class=SpellE>chebyschev</span> part of the background. The window
    15501558should look like</p>
    15511559
    … …  
    15541562 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    15551563 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
    1556 </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
     1564</v:shape><![endif]--><![if !vml]><img width=536 height=263
    15571565src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
    15581566
    … …  
    15861594new negatives that may appear. Then set all the Pawley refinement flags back on
    15871595(excluding any that lead to a singular matrix) and repeat the refinement. After
    1588 refinement, mine converged to ~5.7% with very few negatives and and the plot
    1589 looked like</p>
    1590 
    1591 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1592  id="Picture_x0020_29" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:507pt;
    1593  height:434.25pt;visibility:visible;mso-wrap-style:square'>
     1596refinement, mine converged to ~5.3% with very few negatives and <span
     1597class=SpellE>and</span> the plot looked like</p>
     1598
     1599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1600 id="_x0000_i1056" type="#_x0000_t75" style='width:525pt;height:450pt;
     1601 visibility:visible;mso-wrap-style:square'>
    15941602 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
    1595 </v:shape><![endif]--><![if !vml]><img border=0 width=676 height=579
    1596 src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1603</v:shape><![endif]--><![if !vml]><img width=700 height=600
     1604src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="_x0000_i1056"><![endif]></span></p>
    15971605
    15981606<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
    … …  
    16531661and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16541662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
    1655 determine the lower threshold and upper limit for charge flipping, respectively.
    1656 The latter is used to avoid “Uranium solutions” in the result. Set this to <b
    1657 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1658 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>10-12</span></b>
    1659 for equal atom problems and larger for heavy atom ones. For sucrose set it to <b
    1660 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1661 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>12.</span></b>
    1662 When ready select <b style='mso-bidi-font-weight:normal'><span
    1663 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1664 mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>; a
    1665 progress bar dialog will appear that tracks the residual found in each charge
    1666 flipping cycle. It will quickly drop to some level (42-44%) and then for a
    1667 successful charge flipping run perhaps drop again into the 20-25% range after a
    1668 considerable length of time. You should save the project if you get an
    1669 apparently good solution. Many times it will not drop below ~40%; just try <b
     1663determine the lower threshold and upper limit for charge flipping,
     1664respectively. The latter is used to avoid “Uranium solutions” in the result.
     1665Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1666"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1667minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
     1668ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
     1669style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1670mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
    16701671style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16711672mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
    1672 flipping</span></b> again. If several tries fail to yield a solution, go back
    1673 to the last step of the Pawley refinement and just repeat it (that is do <b
    1674 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1675 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
    1676 update</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1677 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1678 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). This will
    1679 generate a different set of intensities for the highly overlapped part of the
    1680 powder pattern; perhaps they will give a successful charge flip solution.
    1681 Unless otherwise interrupted, GSAS-II will try 10000 times for a charge flip solution
    1682 (for sucrose this takes 5-10min on my laptop). Press <b style='mso-bidi-font-weight:
    1683 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1684 minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
    1685 charge flipping; a peak list and a drawing of the solution will appear. One of
    1686 my runs gave</p>
     1673flipping</span></b>; a progress bar dialog will appear that tracks the residual
     1674found in each charge flipping cycle. It will quickly drop to some level
     1675(42-44%) and then for a successful charge flipping run perhaps drop again into
     1676the 20-25% range after a considerable length of time. You should save the
     1677project if you get an apparently good solution. Many times it will not drop
     1678below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
     1679style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1680mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
     1681several tries fail to yield a solution, go back to the last step of the Pawley
     1682refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
     1683style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1684mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
     1685style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1686mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
     1687This will generate a different set of intensities for the highly overlapped
     1688part of the powder pattern; perhaps they will give a successful charge flip
     1689solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
     1690charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
     1691style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1692mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
     1693to stop the charge flipping; a peak list and a drawing of the solution will
     1694appear. One of my runs gave</p>
    16871695
    16881696<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    16901698 height:225pt;visibility:visible;mso-wrap-style:square'>
    16911699 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image010.png" o:title=""/>
    1692 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
     1700</v:shape><![endif]--><![if !vml]><img width=450 height=300
    16931701src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
    16941702
    … …  
    18021810 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
    18031811  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
    1804 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
     1812</v:shape><![endif]--><![if !vml]><img width=670 height=575
    18051813src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
    18061814
    … …  
    18101818flipping also will give a solution without regard to handedness; this solution
    18111819may be either the correct one for sucrose or its inverse.) Errors in these
    1812 phases can disrupt this process so that the map and peak positions are offset from
    1813 their true positions. To discover this and fix it, rotate the drawing around to
    1814 check that atom positions are related via the 2<sub>1</sub> screw axis (through
    1815 the multicolored cross in the center of the cell and parallel to the y-axis –
    1816 the green cell edge). Avoid motions with the right mouse button pressed, this
    1817 moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
    1818 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1819 mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
    1820 cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my drawing
    1821 above to show where I think it should be. If you find an offset to the map,
    1822 orient it so the offset is horizontal or vertical and then press the <b
     1820phases can disrupt this process so that the map and peak positions are offset
     1821from their true positions. To discover this and fix it, rotate the drawing
     1822around to check that atom positions are related via the 2<sub>1</sub> screw
     1823axis (through the multicolored cross in the center of the cell and parallel to
     1824the y-axis – the green cell edge). Avoid motions with the right mouse button
     1825pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
     1826normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1827minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
     1828cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
     1829drawing above to show where I think it should be. If you find an offset to the
     1830map, orient it so the offset is horizontal or vertical and then press the <b
    18231831style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18241832mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
    … …  
    18421850 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
    18431851  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
    1844 </v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
     1852</v:shape><![endif]--><![if !vml]><img width=667 height=566
    18451853src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
    18461854
    … …  
    18501858the map and make atoms out of them. The map peak list is initially sorted by
    18511859peak magnitude; you can change the sorting to be along any of the column
    1852 headings in the table by a single click on the desired heading. The <b
    1853 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1854 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
    1855 column gives the distance of each peak from the origin. The menu items under
    1856 Map peaks give you several tools to aid in the peak selection process; we will
    1857 just use a couple in this example. I have chosen to proceed by sorting the
    1858 atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1859 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>,
    1860 selecting all and then finding the unique ones. </p>
     1860headings in the table by a single click on the desired heading. The <span
     1861class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1862"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1863minor-latin'>dzero</span></b></span> column gives the distance of each peak
     1864from the origin. The menu items under Map peaks give you several tools to aid
     1865in the peak selection process; we will just use a couple in this example. I
     1866have chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:
     1867normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1868minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and
     1869then finding the unique ones. </p>
    18611870
    18621871<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    18821891should select (grey) 23 out of 46 peak positions in the table and all should be
    18831892near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
    1884 that would be all the C &amp; O atoms! They will be colored green in the plot. If
    1885 more are selected then check the map offset – it may need a slight correction.</p>
     1893that would be all the C &amp; O atoms! They will be colored green in the plot.
     1894If more are selected then check the map offset – it may need a slight
     1895correction.</p>
    18861896
    18871897<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18891899 height:411.75pt;visibility:visible;mso-wrap-style:square'>
    18901900 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
    1891 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549
     1901</v:shape><![endif]--><![if !vml]><img width=450 height=549
    18921902src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
    18931903
    … …  
    18991909 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
    19001910  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
    1901 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
     1911</v:shape><![endif]--><![if !vml]><img width=672 height=572
    19021912src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    19031913
    … …  
    19251935 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
    19261936  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
    1927 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
     1937</v:shape><![endif]--><![if !vml]><img width=672 height=578
    19281938src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
    19291939
    … …  
    19321942 height:414.75pt;visibility:visible;mso-wrap-style:square'>
    19331943 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
    1934 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553
     1944</v:shape><![endif]--><![if !vml]><img width=700 height=553
    19351945src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
    19361946
    … …  
    19461956mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
    19471957normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1948 minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
    1949 and then selecting a position in the table with the <b style='mso-bidi-font-weight:
     1958minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down and
     1959then selecting a position in the table with the <b style='mso-bidi-font-weight:
    19501960normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19511961minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
    … …  
    19621972 height:417pt;visibility:visible;mso-wrap-style:square'>
    19631973 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
    1964 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556
     1974</v:shape><![endif]--><![if !vml]><img width=700 height=556
    19651975src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
    19661976
    … …  
    19831993 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
    19841994  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
    1985 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
     1995</v:shape><![endif]--><![if !vml]><img width=672 height=541
    19861996src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
    19871997
    1988 <p class=MsoNormal>The original charge flipping solution is still visible and the
    1989 atoms are now identified, I’ve changed the drawing to show balls and sticks and
    1990 labeled the atoms with their names, this is done in the <b style='mso-bidi-font-weight:
    1991 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1992 minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b> tab. Double
    1993 click the appropriate column heading and make the selection from the dialog
    1994 box.<span style='mso-spacerun:yes'>  </span></p>
     1998<p class=MsoNormal>The original charge flipping solution is still visible and
     1999the atoms are now identified, I’ve changed the drawing to show balls and sticks
     2000and labeled the atoms with their names, this is done in the <b
     2001style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2002mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
     2003tab. Double click the appropriate column heading and make the selection from
     2004the dialog box.<span style='mso-spacerun:yes'>  </span></p>
    19952005
    19962006<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    19982008 height:415.5pt;visibility:visible;mso-wrap-style:square'>
    19992009 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
    2000 </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554
     2010</v:shape><![endif]--><![if !vml]><img width=600 height=554
    20012011src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
    20022012
    … …  
    20072017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20082018mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
    2009 charge flip map (do <b style='mso-bidi-font-weight:normal'><span
    2010 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2011 mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b
     2019charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     2020style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2021mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
     2022normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2023minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
    20122024style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20132025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    … …  
    20682080style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20692081mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
    2070 selections and make note of the <b style='mso-bidi-font-weight:normal'><span
    2071 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2072 mso-hansi-theme-font:minor-latin'>Sym Op</span></b> for each one. In my case
    2073 they were “<b style='mso-bidi-font-weight:normal'><span style='font-family:
     2082selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
     2083normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2084minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
     2085style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2086mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
     2087for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
     2088style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2089mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
     2090for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
    20742091"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2075 minor-latin'>2+1,0,0</span></b>” for O(4) and “<b style='mso-bidi-font-weight:
    2076 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2077 minor-latin;mso-hansi-theme-font:minor-latin'>2+2,-1,1</span></b>” for O(3).
    2078 The first number is the symmetry operator number and the 3 numbers after the ‘<b
    2079 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2080 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’
    2081 are unit cell translations.</p>
     2092minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
     2093operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
     2094normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2095minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
     2096translations.</p>
    20822097
    20832098<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    20922107"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    20932108</span></span></span><![endif]>Select an atom in turn that needs to be moved,
    2094 e.g. in my case O(3) or O(4). </p>
     2109e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
    20952110
    20962111<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    21152130style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21162131mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
    2117 completed molecule. I’ve made it a balls &amp; sticks with names as labels.</p>
     2132completed <span class=GramE>molecule.</span> I’ve made it a balls &amp; sticks
     2133with names as labels.</p>
    21182134
    21192135<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    21222138 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
    21232139  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
    2124 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
     2140</v:shape><![endif]--><![if !vml]><img width=672 height=576
    21252141src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    21262142
    … …  
    21342150accurate and prepare a set of calculated structure factors needed to generate a
    21352151difference Fourier map good enough to maybe reveal the H atoms. There are a
    2136 number of steps needed to set all the controls from the previous Pawley
    2137 refinement to get a successful start for the Rietveld refinement.</p>
     2152number of steps needed to set all the controls from the previous Pawley refinement
     2153to get a successful start for the Rietveld refinement.</p>
    21382154
    21392155<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    21582174scale factor</span></b> box. This is the scale factor for the data set. Uncheck
    21592175the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2160 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
    2161 displ</span></b>.</p>
     2176mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     2177class=SpellE>displ</span></span></b>.</p>
    21622178
    21632179<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    21782194style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21792195mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    2180 GSAS-II data tree menu; only scale and background are refined. I got a Rwp
    2181 ~20%. The plot shows clear intensity differences; the atom positions obviously
    2182 need refinement.</p>
    2183 
    2184 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2185  id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt;
    2186  height:430.5pt;visibility:visible;mso-wrap-style:square'>
     2196GSAS-II data tree menu; only scale and background are refined. I got <span
     2197class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
     2198intensity differences; the atom positions obviously need refinement.</p>
     2199
     2200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2201 id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
     2202 visibility:visible;mso-wrap-style:square'>
    21872203 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
    2188 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574
    2189 src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
     2204</v:shape><![endif]--><![if !vml]><img width=700 height=600
     2205src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1044"><![endif]></span></p>
    21902206
    21912207<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
    … …  
    22122228 height:225pt;visibility:visible;mso-wrap-style:square'>
    22132229 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
    2214 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
     2230</v:shape><![endif]--><![if !vml]><img width=700 height=300
    22152231src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
    22162232
    … …  
    22252241 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    22262242 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
    2227 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
     2243</v:shape><![endif]--><![if !vml]><img width=300 height=250
    22282244src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
    22292245
    … …  
    22322248mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
    22332249style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2234 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0::dAy:0 for
    2235 O(1)</span></b>’ from the dialog box. This will fix the shift along y for the
    2236 O(1) atom.</p>
     2250mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
     2251class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
     2252fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
    22372253
    22382254<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    22402256 height:271.5pt;visibility:visible;mso-wrap-style:square'>
    22412257 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
    2242 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
     2258</v:shape><![endif]--><![if !vml]><img width=346 height=362
    22432259src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
    22442260
    … …  
    22522268 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    22532269 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
    2254 </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
     2270</v:shape><![endif]--><![if !vml]><img width=300 height=250
    22552271src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
    22562272
    22572273<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    22582274style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2259 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is
    2260 now ~10.3%. You can now safely refine lattice parameters (in the <b
    2261 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2262 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    2263 tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2275mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
     2276class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
     2277parameters (in the <b style='mso-bidi-font-weight:normal'><span
     2278style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2279mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
     2280style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22642281mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
    22652282the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    … …  
    22772294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    22782295and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2279 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
    2280 displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>)
    2281 parameters. My refinement improved slightly to Rwp~10.0%. Let’s see if a
    2282 difference Fourier map will show anything.<br>
     2296mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     2297class=SpellE>displ</span></span></b>. You can also include refinement of atom
     2298thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
     2299refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
     2300map will show anything.<br>
    22832301Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22842302mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
    … …  
    22912309mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    22922310"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2293 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    2294 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2295 mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b
    2296 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2311</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
     2312normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2313minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
     2314style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2315mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
     2316for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22972317mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
    22982318
    … …  
    23422362 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
    23432363  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
    2344 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
     2364</v:shape><![endif]--><![if !vml]><img width=670 height=581
    23452365src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
    23462366
    … …  
    23572377</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    23582378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2359 mso-hansi-theme-font:minor-latin'>Phases/sucrose<span
    2360 style='mso-spacerun:yes'>  </span>Draw Atoms</span></b> tab.</p>
     2379mso-hansi-theme-font:minor-latin'>Phases/sucrose Draw Atoms</span></b> tab.</p>
    23612380
    23622381<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    … …  
    23882407 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
    23892408  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
    2390 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
     2409</v:shape><![endif]--><![if !vml]><img width=672 height=581
    23912410src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    23922411
    … …  
    24102429 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
    24112430  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
    2412 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
     2431</v:shape><![endif]--><![if !vml]><img width=672 height=570
    24132432src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
    24142433
    … …  
    24242443style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24252444mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2426 there should be a drop in Rwp. Then repeat the <b style='mso-bidi-font-weight:
    2427 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2428 minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> in
    2429 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2430 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    2431 tab, adjust the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2432 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2433 minor-latin'>Contour level</span></b> and <b style='mso-bidi-font-weight:normal'><span
    2434 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2435 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the
    2436 remaining H-atoms; you may have to guess positions for some of them using known
    2437 stereochemistry rules. My model looked like</p>
     2445there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
     2446style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2447mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
     2448map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
     2449style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2450mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
     2451style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2452mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
     2453level</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2454style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2455mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
     2456the remaining H-atoms; you may have to guess positions for some of them using
     2457known stereochemistry rules. My model looked like</p>
    24382458
    24392459<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    24422462 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
    24432463  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
    2444 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
     2464</v:shape><![endif]--><![if !vml]><img width=670 height=562
    24452465src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
    24462466
    … …  
    24482468style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    24492469mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
    2450 stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms
    2451 included (but not refined). The fit looks pretty good</p>
     2470stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
     2471with all the H-atoms included (but not refined). The fit looks pretty good</p>
    24522472
    24532473<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    24552475 height:450pt;visibility:visible;mso-wrap-style:square'>
    24562476 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
    2457 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     2477</v:shape><![endif]--><![if !vml]><img width=700 height=600
    24582478src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
    24592479
    … …  
    24622482<p class=MsoNormal>Looking at the fit, there may be room for improvement and
    24632483we’d like to refine the H-atom positions. First we need to change the profile
    2464 model to include crystallite size and mustrain broadening. Go to <b
    2465 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2466 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    2467 Parameters</span></b>, set <b style='mso-bidi-font-weight:normal'><span
    2468 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2469 mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
    2470 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2471 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> to <b
    2472 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2484model to include crystallite size and <span class=SpellE>mustrain</span>
     2485broadening. Go to <b style='mso-bidi-font-weight:normal'><span
     2486style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2487mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
     2488style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2489mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     2490and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2491mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
     2492to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24732493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
    24742494and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    … …  
    24842504style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    24852505mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
    2486 boxes for both <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2487 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2488 minor-latin'>Cryst. size</span></b> and <b style='mso-bidi-font-weight:normal'><span
    2489 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2490 mso-hansi-theme-font:minor-latin'>microstrain</span></b>.</p>
     2506boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2507style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2508mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
     2509normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2510minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
     2511and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2512style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2513mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
    24912514
    24922515<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    24942517 height:339pt;visibility:visible;mso-wrap-style:square'>
    24952518 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
    2496 </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452
     2519</v:shape><![endif]--><![if !vml]><img width=640 height=452
    24972520src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
    24982521
    24992522<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    25002523style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2501 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
    2502 start out high but should converge to where it was before this change. I got
    2503 8.08% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2504 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2505 minor-latin'>Data tab</span></b> looked like</p>
     2524mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
     2525class=SpellE>Rwp</span> will start out high but should converge to where it was
     2526before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
     2527style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2528mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
    25062529
    25072530<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    25092532 height:334.5pt;visibility:visible;mso-wrap-style:square'>
    25102533 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
    2511 </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446
     2534</v:shape><![endif]--><![if !vml]><img width=640 height=446
    25122535src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
    25132536
    25142537<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
    25152538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2516 mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <b
    2517 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2518 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain
    2519 model</span></b>; this is the Stephens phenomenological model for microstrain
    2520 which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
     2539mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
     2540class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2541"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2542minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
     2543style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2544mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
     2545phenomenological model for <span class=SpellE>microstrain</span> which has 9
     2546terms for monoclinic structures. Check all the boxes for it.</p>
    25212547
    25222548<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    25242550 height:303.75pt;visibility:visible;mso-wrap-style:square'>
    25252551 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
    2526 </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405
     2552</v:shape><![endif]--><![if !vml]><img width=640 height=405
    25272553src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
    25282554
    25292555<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    25302556style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2531 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
    2532 start out high but should converge lower than where it was before this change.
    2533 I got 7.65% and the <b style='mso-bidi-font-weight:normal'><span
    2534 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2535 mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. If you check
    2536 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2537 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain</span></b>
    2538 button in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2539 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2540 minor-latin'>Select plot type</span></b> box, you will see the interesting
    2541 mustrain surface plot for ground sucrose.</p>
     2557mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
     2558class=SpellE>Rwp</span> will start out high but should converge lower than
     2559where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
     2560normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2561minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
     2562If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2563style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2564mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
     2565style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
     2567type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
     2568surface plot for ground sucrose.</p>
    25422569
    25432570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    25452572 height:305.25pt;visibility:visible;mso-wrap-style:square'>
    25462573 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
    2547 </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407
     2574</v:shape><![endif]--><![if !vml]><img width=640 height=407
    25482575src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
    25492576
    … …  
    25542581 height:450pt;visibility:visible;mso-wrap-style:square'>
    25552582 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
    2556 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
     2583</v:shape><![endif]--><![if !vml]><img width=700 height=600
    25572584src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
    25582585
    … …  
    25712598 height:252pt;visibility:visible;mso-wrap-style:square'>
    25722599 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
    2573 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
     2600</v:shape><![endif]--><![if !vml]><img width=346 height=336
    25742601src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
    25752602
    … …  
    25852612 height:252pt;visibility:visible;mso-wrap-style:square'>
    25862613 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
    2587 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
     2614</v:shape><![endif]--><![if !vml]><img width=346 height=336
    25882615src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
    25892616
    … …  
    25992626 height:78.75pt;visibility:visible;mso-wrap-style:square'>
    26002627 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
    2601 </v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105
     2628</v:shape><![endif]--><![if !vml]><img width=196 height=105
    26022629src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
    26032630style='mso-spacerun:yes'> </span></p>
    … …  
    26222649 height:423pt;visibility:visible;mso-wrap-style:square'>
    26232650 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
    2624 </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564
     2651</v:shape><![endif]--><![if !vml]><img width=600 height=564
    26252652src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
    26262653
    … …  
    26522679 height:365.25pt;visibility:visible;mso-wrap-style:square'>
    26532680 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
    2654 </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487
     2681</v:shape><![endif]--><![if !vml]><img width=600 height=487
    26552682src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
    26562683
    … …  
    26732700style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    26742701mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
    2675 list progress on the “Penalty function” (i.e. the restraints) and the Rwp drops
    2676 in my case to ~7.05%. One can increase the <b style='mso-bidi-font-weight:normal'><span
    2677 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2678 mso-hansi-theme-font:minor-latin'>Restraint weight factors</span></b> to
    2679 tighten them up at some expense in Rwp. In the end I chose <b style='mso-bidi-font-weight:
     2702list progress on the “Penalty function” (i.e. the restraints) and the <span
     2703class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
     2704style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2705mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
     2706weight factors</span></b> to tighten them up at some expense in <span
     2707class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
    26802708normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    26812709minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
    … …  
    26842712and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    26852713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
    2686 restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be
    2687 correct even though the refinement apparently succeeded. You should check that
    2688 the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is
    2689 powder data such changes will hardly affect the fit but will be more
     2714restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
     2715positions may not be correct even though the refinement apparently succeeded.
     2716You should check that the OH ones all give reasonable H-bonds to neighboring O-atoms.
     2717As this is powder data such changes will hardly affect the fit but will be more
    26902718satisfying. At present such checking is outside the scope of GSAS-II.</p>
    26912719
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