Changeset 872


Ignore:
Timestamp:
Mar 22, 2013 10:24:31 AM (9 years ago)
Author:
vondreele
Message:

cleanup tutorial

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/Charge Flipping - sucrose.htm

    r870 r872  
    2424  <o:Author>Von Dreele</o:Author>
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    26   <o:Revision>13</o:Revision>
    27   <o:TotalTime>1342</o:TotalTime>
     26  <o:Revision>14</o:Revision>
     27  <o:TotalTime>1423</o:TotalTime>
    2828  <o:Created>2013-03-15T18:32:00Z</o:Created>
    29   <o:LastSaved>2013-03-21T16:12:00Z</o:LastSaved>
     29  <o:LastSaved>2013-03-22T15:24:00Z</o:LastSaved>
    3030  <o:Pages>17</o:Pages>
    31   <o:Words>3395</o:Words>
    32   <o:Characters>19358</o:Characters>
     31  <o:Words>3367</o:Words>
     32  <o:Characters>19197</o:Characters>
    3333  <o:Company>Argonne National Laboratory</o:Company>
    34   <o:Lines>161</o:Lines>
     34  <o:Lines>159</o:Lines>
    3535  <o:Paragraphs>45</o:Paragraphs>
    36   <o:CharactersWithSpaces>22708</o:CharactersWithSpaces>
     36  <o:CharactersWithSpaces>22519</o:CharactersWithSpaces>
    3737  <o:Version>14.00</o:Version>
    3838 </o:DocumentProperties>
     
    953953fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
    954954
    955 <h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
     955<h2>Step 1: Setup for Pawley refinement</h2>
    956956
    957957<p class=MsoNormal>There are a number of steps that must be done in preparation
     
    969969Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
    970970mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
    971 symbol;mso-symbol-font-family:Symbol'>Q</span></span>. It is an area relatively
    972 clear of peaks and makes a good place to end the calculations with a reflection
    973 set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
    974 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    975 minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span
    976 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    977 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    978 minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
    979 exact d-spacing (1.0125Å) using the mouse cursor on the plot.</p>
     971symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
     972relatively clear of peaks that makes a good place to end the calculations with
     973a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution needed
     974for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
     975style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     976mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
     977style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
     979as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
     980mouse cursor on the plot.</p>
    980981
    981982<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
     
    10211022normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    10221023minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
    1023 box and enter the d-spacing (1.0125) into the <b style='mso-bidi-font-weight:
    1024 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1025 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
    1026 box.</p>
     1024box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
     1025style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1026mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
     1027style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1028mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1029class=SpellE>dmin</span></span></b> box.</p>
    10271030
    10281031<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    10931096surfaces</p>
    10941097
    1095 <p class=MsoNormal><span class=GramE>and</span> preferred orientation
     1098<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
    10961099correction curves.</p>
    10971100
     
    11191122you didn’t skip a step as it might not work correctly if you did.</p>
    11201123
    1121 <h2>Step 2 Pawley refinement</h2>
     1124<h2>Step 2: Pawley refinement</h2>
    11221125
    11231126<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
     
    11971200
    11981201<p class=MsoNormal>What you see is that the background has a substantial
    1199 diffuse scattering feature at ~5deg as well as some peak shape issues (which
    1200 may be a consequence of the poor background fit). Also notice the negative <b
    1201 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1202 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    1203 value in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1204 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    1205 parameters</span></b>; the problem is that the default <span class=SpellE>mustrain</span>
    1206 value (1000.0) is much too high for this material and we’d like the fit to be
     1202diffuse scattering feature at ~5deg and there are some peak shape issues (which
     1203may be a consequence of the poor background fit). We’d like the fit to be
    12071204better before trying charge flipping. First select <span class=GramE><b
    12081205style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    12631260normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    12641261minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
    1265 the refinement converges. After a set of refinement cycles go to the Pawley reflections
     1262the refinement converges. After a set of refinement cycles go to the <b
     1263style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b>
    12661265tab and check the intensities. If there are many negatives amongst the highest
    12671266angle reflections do <b style='mso-bidi-font-weight:normal'><span
    12681267style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    12691268mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all
    1270 the values with those in the extracted from the profile and listed in the <b
     1269the values with those in the extracted from the profile as listed in the <b
    12711270style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    12721271mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    1273 list</span></b> for the PWDR data set. Next in the <b style='mso-bidi-font-weight:
    1274 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1275 minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab set the <b
     1272list</span></b> for the PWDR data set. This makes all the negative intensities
     1273positive. Next in the <b style='mso-bidi-font-weight:normal'><span
     1274style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1275mso-hansi-theme-font:minor-latin'>General</span></b> tab set the <b
    12761276style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    12771277mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley neg.
     
    12931293<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
    12941294
    1295 <h2>Step 3 Charge flipping</h2>
     1295<h2>Step 3: Charge flipping</h2>
    12961296
    12971297<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
     
    13171317style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    13181318mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
    1319 data set; these should match the Pawley reflection set.</p>
     1319data set; these should match the <b style='mso-bidi-font-weight:normal'><span
     1320style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1321mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
    13201322
    13211323<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    13511353"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    13521354minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
    1353 ones. <span class=GramE>For sucrose, set this to <b style='mso-bidi-font-weight:
    1354 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1355 minor-latin;mso-hansi-theme-font:minor-latin'>12.</span></b></span> When ready
    1356 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1355ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
     1356style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1357mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
     1358style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    13571359mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
    13581360flipping</span></b>; a progress bar dialog will appear that tracks the residual
    13591361found in each charge flipping cycle. It will quickly drop to some level
    1360 (42-44%) and then perhaps drop again into the 20-25% range after a considerable
    1361 length of time for a successful charge flipping run. You should save the
     1362(42-44%) and then for a successful charge flipping run perhaps drop again into
     1363the 20-25% range after a considerable length of time. You should save the
    13621364project if you get an apparently good solution. Many times it will not drop
    13631365below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
     
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    15001502<p class=MsoNormal>The result looks very promising! Charge flipping operates
    15011503without regard to symmetry and GSAS-II attempts to locate the map with respect
    1502 to the symmetry elements from the computed reflection phases. NB: charge
    1503 flipping also will give a solution without regard to handedness. This solution
    1504 may be either the correct one for sucrose or its reverse. Errors in these
     1504to the symmetry elements from the computed reflection phases. (NB: charge
     1505flipping also will give a solution without regard to handedness; this solution
     1506may be either the correct one for sucrose or its inverse.) Errors in these
    15051507phases can disrupt this process so that the map and peak positions are offset
    15061508from their true positions. To discover this and fix it, rotate the drawing
     
    15381540src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
    15391541
    1540 <h2>Step 4 Obtain solution from charge flip result</h2>
     1542<h2>Step 4: Obtain solution from charge flip result</h2>
    15411543
    15421544<p class=MsoNormal>The next step is to extract the unique peak positions from
    1543 the map and make atoms out of them. The map peak list is sorted with the
    1544 highest peak first; you can change the sorting to be along any of the column
     1545the map and make atoms out of them. The map peak list is initially sorted by
     1546peak magnitude; you can change the sorting to be along any of the column
    15451547headings in the table by a single click on the desired heading. The <span
    15461548class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     
    16521654src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
    16531655
    1654 <p class=MsoNormal>Notice that in this case the atom list is neatly sorted out into
    1655 two groups with a clear gap between M79 and M64. The higher ones are likely to
    1656 be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
    1657 ambiguity in the middle, but just assign the top 11 as O and the rest as C and
    1658 see what happens. You can do this by selecting a block of atoms, go to <b
     1656<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
     1657into two groups with a clear gap between M79 and M64. The higher ones are
     1658likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
     1659of ambiguity in the middle, but just assign the top 11 as O and the rest as C
     1660and see what happens. You can do this by selecting a block of atoms, go to <b
    16591661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16601662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
     
    16781680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16791681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
    1680 tab. Pick the appropriate column and make the selection from the dialog
    1681 box.<span style='mso-spacerun:yes'>  </span></p>
     1682tab. Double click the appropriate column heading and make the selection from
     1683the dialog box.<span style='mso-spacerun:yes'>  </span></p>
    16821684
    16831685<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16881690src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
    16891691
    1690 <p class=MsoNormal>Interestingly the atoms identified exactly matched with the
    1691 magnitudes of the charge flip map peaks with O at the top and C at the bottom.</p>
    1692 
    16931692<p class=MsoNormal>Now one can safely remove the map peaks (do <b
    16941693style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    17481747they will probably be outside the unit cell box. Do this on the drawing with <b
    17491748style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1750 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
    1751 left &amp; right mouse buttons, they will show in green. </p>
     1749mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
     1750for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
     1751style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1752mso-hansi-theme-font:minor-latin'>Shift right</span></b> for <span
     1753class=SpellE>the</span> rest, they will show in green. </p>
    17521754
    17531755<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18191821src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    18201822
    1821 <p class=MsoNormal>Save the project file; the next step is to <span
    1822 class=GramE>do<span style='mso-spacerun:yes'>  </span>the</span> Rietveld
    1823 refinement on the completed structure.</p>
    1824 
    1825 <h2>Step 5 Complete the structure</h2>
     1823<p class=MsoNormal>Save the project file; the next step is to complete the
     1824structure by finding H-atoms and then do the final Rietveld refinements.</p>
     1825
     1826<h2>Step 5: Complete the structure</h2>
    18261827
    18271828<p class=MsoNormal>To complete the structure you will need to perform a
     
    18731874style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    18741875mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    1875 GSAS-II data tree menu; all that was refined is scale and background. I got <span
     1876GSAS-II data tree menu; only scale and background are refined. I got <span
    18761877class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
    18771878intensity differences; the atom positions obviously need refinement.</p>
     
    18921893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18931894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
    1894 tab. Note the warning at the bottom of the window; the origin in space group P
    1895 2<sub>1</sub> has an arbitrary location along the y-axis. Then double click the
    1896 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1895tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
     1896has an arbitrary location along the y-axis. Then double click the <b
     1897style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18971898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
    18981899column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
     
    20042005the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    20052006mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    2006 set from</span></b> item (the only choice). The Fourier calculation will use the
    2007 structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
     2007set from</span></b> item (the only choice). The Fourier calculation will use
     2008the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
    20082009style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20092010mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
     
    20492050position. Recall that the refinement was just done without any H-atoms; it will
    20502051make the best fit compensating for the missing H-atoms by displacing the C
    2051 &amp;O atoms in the direction of the missing H-atoms. </p>
     2052&amp; O atoms in the direction of the missing H-atoms. </p>
    20522053
    20532054<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20622063mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    20632064"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2064 </span></span></span><![endif]>Select a C or O atoms with possible H-atom
     2065</span></span></span><![endif]>Select a C or O atom with possible H-atom
    20652066density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
    20662067style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     
    21022103recognizable H-atom positions you can find; the goal is to find all 22 of them
    21032104(you probably will find less than that, but you could guess many of the rest).
    2104 I found all but 5 of them.</p>
     2105I easily found all but 5 of them.</p>
    21052106
    21062107<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21302131mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
    21312132style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2132 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour level</span></b>
    2133 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2134 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
    2135 as desired. Look for the remaining H-atoms; you may have to guess positions for
    2136 some of them using known stereochemistry rules. My model looked like</p>
     2133mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
     2134level</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2135style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2136mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
     2137the remaining H-atoms; you may have to guess positions for some of them using
     2138known stereochemistry rules. My model looked like</p>
    21372139
    21382140<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22032205mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    22042206class=SpellE>Rwp</span> will start out high but should converge to where it was
    2205 before this change. I got 8.08% and the Data tab looked like</p>
     2207before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
     2208style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2209mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
    22062210
    22072211<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22122216src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
    22132217
    2214 <p class=MsoNormal>This no change in model yet but next select <b
    2215 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2216 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Generalized</span></b>
    2217 for the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2218 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2219 mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span><b
    2220 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2221 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> model</span></b>;
    2222 this is the Stephens phenomenological model for <span class=SpellE>microstrain</span>
    2223 which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
     2218<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
     2219style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2220mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
     2221class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2222"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2223minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
     2224style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2225mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
     2226phenomenological model for <span class=SpellE>microstrain</span> which has 9
     2227terms for monoclinic structures. Check all the boxes for it.</p>
    22242228
    22252229<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22342238mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    22352239class=SpellE>Rwp</span> will start out high but should converge lower than
    2236 where it was before this change. I got 7.65% and the Data tab looked like. If
    2237 you check the <span class=SpellE>Mustrain</span> button in the Select plot type
    2238 box, you will see the interesting <span class=SpellE>mustrain</span> surface
    2239 plot for ground sucrose.</p>
     2240where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
     2241normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2242minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
     2243If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2244style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2245mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
     2246style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2247mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
     2248type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
     2249surface plot for ground sucrose.</p>
    22402250
    22412251<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    23412351normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    23422352minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
    2343 tetrahedral angle so just press OK. 36 restraints will be listed; they are
    2344 listed in order of the B atom. O-atoms should have one angle apiece; C-atoms
    2345 will have more. </p>
     2353tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
     2354style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2355mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
     2356they are listed in order of the B atom. O-atoms should have one angle apiece;
     2357C-atoms will have more. </p>
    23462358
    23472359<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    23672379style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    23682380mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
    2369 for all H-atoms. Now do <span style='font-family:"Calibri","sans-serif";
    2370 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span>,
    2371 the console will list progress on the “Penalty function” (i.e. the restraints)
    2372 and the <span class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase
    2373 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2381for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
     2382style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2383mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
     2384list progress on the “Penalty function” (i.e. the restraints) and the <span
     2385class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
     2386style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    23742387mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
    23752388weight factors</span></b> to tighten them up at some expense in <span
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