Changeset 1717


Ignore:
Timestamp:
Mar 16, 2015 4:10:20 PM (8 years ago)
Author:
vondreele
Message:

update the sucrose images

Location:
Tutorials/CFsucrose
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CFsucrose/Charge Flipping - sucrose.htm

    r1705 r1717  
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     130  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     131   UnhideWhenUsed="true" Name="toc 4"/>
     132  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     133   UnhideWhenUsed="true" Name="toc 5"/>
     134  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     135   UnhideWhenUsed="true" Name="toc 6"/>
     136  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     137   UnhideWhenUsed="true" Name="toc 7"/>
     138  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     139   UnhideWhenUsed="true" Name="toc 8"/>
     140  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     141   UnhideWhenUsed="true" Name="toc 9"/>
     142  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     143   Name="Normal Indent"/>
     144  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     145   Name="footnote text"/>
     146  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     147   Name="annotation text"/>
     148  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     149   Name="header"/>
     150  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     151   Name="footer"/>
     152  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     153   Name="index heading"/>
     154  <w:LsdException Locked="false" Priority="35" SemiHidden="true"
     155   UnhideWhenUsed="true" QFormat="true" Name="caption"/>
     156  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     157   Name="table of figures"/>
     158  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     159   Name="envelope address"/>
     160  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     161   Name="envelope return"/>
     162  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     163   Name="footnote reference"/>
     164  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     165   Name="annotation reference"/>
     166  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     167   Name="line number"/>
     168  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     169   Name="page number"/>
     170  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     171   Name="endnote reference"/>
     172  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     173   Name="endnote text"/>
     174  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     175   Name="table of authorities"/>
     176  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     177   Name="macro"/>
     178  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     179   Name="toa heading"/>
     180  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     181   Name="List"/>
     182  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     183   Name="List Bullet"/>
     184  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     185   Name="List Number"/>
     186  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     187   Name="List 2"/>
     188  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     189   Name="List 3"/>
     190  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     191   Name="List 4"/>
     192  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     193   Name="List 5"/>
     194  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     195   Name="List Bullet 2"/>
     196  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     197   Name="List Bullet 3"/>
     198  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     199   Name="List Bullet 4"/>
     200  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     201   Name="List Bullet 5"/>
     202  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     203   Name="List Number 2"/>
     204  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     205   Name="List Number 3"/>
     206  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     207   Name="List Number 4"/>
     208  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     209   Name="List Number 5"/>
     210  <w:LsdException Locked="false" Priority="10" QFormat="true" Name="Title"/>
     211  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     212   Name="Closing"/>
     213  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     214   Name="Signature"/>
     215  <w:LsdException Locked="false" Priority="1" SemiHidden="true"
     216   UnhideWhenUsed="true" Name="Default Paragraph Font"/>
     217  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     218   Name="Body Text"/>
     219  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     220   Name="Body Text Indent"/>
     221  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     222   Name="List Continue"/>
     223  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     224   Name="List Continue 2"/>
     225  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     226   Name="List Continue 3"/>
     227  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     228   Name="List Continue 4"/>
     229  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     230   Name="List Continue 5"/>
     231  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     232   Name="Message Header"/>
     233  <w:LsdException Locked="false" Priority="11" QFormat="true" Name="Subtitle"/>
     234  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     235   Name="Salutation"/>
     236  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     237   Name="Date"/>
     238  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     239   Name="Body Text First Indent"/>
     240  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     241   Name="Body Text First Indent 2"/>
     242  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     243   Name="Note Heading"/>
     244  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     245   Name="Body Text 2"/>
     246  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     247   Name="Body Text 3"/>
     248  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     249   Name="Body Text Indent 2"/>
     250  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     251   Name="Body Text Indent 3"/>
     252  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     253   Name="Block Text"/>
     254  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     255   Name="Hyperlink"/>
     256  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     257   Name="FollowedHyperlink"/>
     258  <w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/>
     259  <w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/>
     260  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     261   Name="Document Map"/>
     262  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     263   Name="Plain Text"/>
     264  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     265   Name="E-mail Signature"/>
     266  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     267   Name="HTML Top of Form"/>
     268  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     269   Name="HTML Bottom of Form"/>
     270  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     271   Name="Normal (Web)"/>
     272  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     273   Name="HTML Acronym"/>
     274  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     275   Name="HTML Address"/>
     276  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     277   Name="HTML Cite"/>
     278  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     279   Name="HTML Code"/>
     280  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     281   Name="HTML Definition"/>
     282  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     283   Name="HTML Keyboard"/>
     284  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     285   Name="HTML Preformatted"/>
     286  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     287   Name="HTML Sample"/>
     288  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     289   Name="HTML Typewriter"/>
     290  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     291   Name="HTML Variable"/>
     292  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     293   Name="Normal Table"/>
     294  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     295   Name="annotation subject"/>
     296  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     297   Name="No List"/>
     298  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     299   Name="Outline List 1"/>
     300  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     301   Name="Outline List 2"/>
     302  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     303   Name="Outline List 3"/>
     304  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     305   Name="Table Simple 1"/>
     306  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     307   Name="Table Simple 2"/>
     308  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     309   Name="Table Simple 3"/>
     310  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     311   Name="Table Classic 1"/>
     312  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     313   Name="Table Classic 2"/>
     314  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     315   Name="Table Classic 3"/>
     316  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     317   Name="Table Classic 4"/>
     318  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     319   Name="Table Colorful 1"/>
     320  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     321   Name="Table Colorful 2"/>
     322  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     323   Name="Table Colorful 3"/>
     324  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     325   Name="Table Columns 1"/>
     326  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     327   Name="Table Columns 2"/>
     328  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     329   Name="Table Columns 3"/>
     330  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     331   Name="Table Columns 4"/>
     332  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     333   Name="Table Columns 5"/>
     334  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     335   Name="Table Grid 1"/>
     336  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     337   Name="Table Grid 2"/>
     338  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     339   Name="Table Grid 3"/>
     340  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     341   Name="Table Grid 4"/>
     342  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     343   Name="Table Grid 5"/>
     344  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     345   Name="Table Grid 6"/>
     346  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     347   Name="Table Grid 7"/>
     348  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     349   Name="Table Grid 8"/>
     350  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     351   Name="Table List 1"/>
     352  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     353   Name="Table List 2"/>
     354  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     355   Name="Table List 3"/>
     356  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     357   Name="Table List 4"/>
     358  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     359   Name="Table List 5"/>
     360  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     361   Name="Table List 6"/>
     362  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     363   Name="Table List 7"/>
     364  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     365   Name="Table List 8"/>
     366  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     367   Name="Table 3D effects 1"/>
     368  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     369   Name="Table 3D effects 2"/>
     370  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     371   Name="Table 3D effects 3"/>
     372  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     373   Name="Table Contemporary"/>
     374  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     375   Name="Table Elegant"/>
     376  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     377   Name="Table Professional"/>
     378  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     379   Name="Table Subtle 1"/>
     380  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     381   Name="Table Subtle 2"/>
     382  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     383   Name="Table Web 1"/>
     384  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     385   Name="Table Web 2"/>
     386  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     387   Name="Table Web 3"/>
     388  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     389   Name="Balloon Text"/>
     390  <w:LsdException Locked="false" Priority="59" Name="Table Grid"/>
     391  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     392   Name="Table Theme"/>
     393  <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/>
     394  <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/>
     395  <w:LsdException Locked="false" Priority="60" Name="Light Shading"/>
     396  <w:LsdException Locked="false" Priority="61" Name="Light List"/>
     397  <w:LsdException Locked="false" Priority="62" Name="Light Grid"/>
     398  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/>
     399  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
     400  <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/>
     401  <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/>
     402  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/>
     403  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/>
     404  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/>
     405  <w:LsdException Locked="false" Priority="70" Name="Dark List"/>
     406  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/>
     407  <w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
     408  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
     409  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
     410  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
     411  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
     412  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
     413  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
     414  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
     415  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
     416  <w:LsdException Locked="false" Priority="34" QFormat="true"
     417   Name="List Paragraph"/>
     418  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
     419  <w:LsdException Locked="false" Priority="30" QFormat="true"
     420   Name="Intense Quote"/>
     421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
     422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
     423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
     424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
     425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
     426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
     427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
     428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
     429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
     430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
     431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
     432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
     433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
     434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
     435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
     436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
     437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
     438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
     439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
     440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
     441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
     442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
     443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
     444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
     445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
     446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
     447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
     448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
     449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
     450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
     451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
     452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
     453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
     454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
     455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
     456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
     457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
     458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
     459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
     460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
     461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
     462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
     463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
     464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
     465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
     466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
     467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
     468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
     469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
     470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
     471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
     472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
     473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
     474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
     475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
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    9461258
    9471259<p class=MsoNormal>If you have not done so already, <a
    948 href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
    949 (I called it <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    950 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    951 mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>) you saved from
    952 the third part of the <a href="Fit%20Peaks.htm#sucrose_peak_fit">peak
     1260href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a> and open the
     1261GSAS-II project file (I called it <b style='mso-bidi-font-weight:normal'><span
     1262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1263mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b>) you saved from the
     1264third part of the <a
     1265href="../../../GSASII/help/Fit%20Peaks.htm#sucrose_peak_fit">peak
    9531266fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
    9541267
     
    9631276style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    9641277style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    965 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1278<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    9661279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
    9671280in the GSAS-II data tree for the PWDR data set and expand the plot so that the
     
    9711284symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
    9721285relatively clear of peaks that makes a good place to end the calculations with
    973 a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
    974 needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
    975 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    976 mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
    977 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    978 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
     1286a reflection set of d<sub>min</sub> ~1Å resolution needed for charge flipping.
     1287Enter <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b>
     1289for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1290mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b>
    9791291as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
    9801292mouse cursor on the plot.</p>
     
    9831295style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    9841296style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    985 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1297<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    9861298mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    9871299Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
    988 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1300style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    9891301mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
    990 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    9911303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
    9921304profile</span></b> to recover the default values. The peak fitting done earlier
     
    10011313style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    10021314style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1003 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1315<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10041316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
    10051317Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
    1006 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1318normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    10071319minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
    10081320While you are here set <b style='mso-bidi-font-weight:normal'><span
    1009 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1321style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10101322mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
    1011 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1323style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10121324mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
    10131325
     
    10151327style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    10161328style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    1017 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1329to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10181330mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
    10191331to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1020 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1332"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    10211333minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
    1022 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1334normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    10231335minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
    10241336box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
    1025 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10261338mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
    1027 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1028 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
    1029 class=SpellE>dmin</span></span></b> box.</p>
     1339style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>
     1341box.</p>
    10301342
    10311343<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
    1032 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10331345mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
    10341346
     
    10601372
    10611373<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    1062 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1374style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10631375mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
    10641376for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
    1065 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1377style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10661378mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
    10671379dialog box will appear</p>
     
    10761388<p class=MsoNormal>Select either choice; the desired data set will be added to
    10771389this phase for analysis. The data tab now shows the new data set; check the <b
    1078 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1390style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10791391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    10801392button to see the full information</p>
     
    10891401<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    10901402contents. This is the location for all the phase dependent parameters for this
    1091 histogram. Notice that it includes phase fraction, size &amp; <span
    1092 class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
    1093 and extinction corrections. The <span class=SpellE>Babinet</span> correction is
    1094 intended for protein work where a significant region of the structure is
    1095 disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
    1096 surfaces</p>
    1097 
    1098 <p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
    1099 correction curves.</p>
     1403histogram. Notice that it includes phase fraction, size &amp; mustrain as well
     1404as preferred orientation, elastic strain and extinction corrections. The
     1405Babinet correction is intended for protein work where a significant region of
     1406the structure is disordered solvent. There are buttons for plotting size and
     1407mustrain surfaces</p>
     1408
     1409<p class=MsoNormal>as well as preferred orientation correction curves.</p>
    11001410
    11011411<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    1102 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1412style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11031413mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
    1104 empty except for column headings. <span class=GramE>Do</span> <b
    1105 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1106 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
    1107 create</span></b>; this makes the reflection set over the range covered by
    1108 setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1109 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
    1110 class=SpellE>dmin</span></span></b>. The table should list reflections 0-781.
    1111 Select and check the refine column using the same technique you used for the
    1112 peak list. </p>
     1414empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
     1415style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1416mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
     1417makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
     1418normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1419minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
     1420should list reflections 0-781. Select and check the refine column using the
     1421same technique you used for the peak list. </p>
    11131422
    11141423<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11251434
    11261435<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
    1127 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1436normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    11281437minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
    11291438the main GSAS-II data tree window. Before it begins a backup of the project
    11301439file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
    1131 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1440style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11321441mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
    11331442to recover from a bad refinement. A progress dialog box will appear showing the
     
    11361445the refinement because it was off the end of the used part of the pattern. This
    11371446is the GSAS-II singular matrix recovery mechanism; you can go to the <b
    1138 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1447style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11391448mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
    11401449reflections</span></b> tab and uncheck the last reflection. Then repeat <b
    1141 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1450style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11421451mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1143 to make sure it has essentially minimized. My refinement completed with <span
    1144 class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
    1145 the result. Press <b style='mso-bidi-font-weight:normal'><span
    1146 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1147 mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
    1148 PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
     1452to 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
     1454style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1456To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
     1457the width and height).</p>
    11491458
    11501459<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11581467can be had by refining the lattice and profile parameters and perhaps the
    11591468sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
    1160 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1469style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11611470mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
    11621471tree and check the <b style='mso-bidi-font-weight:normal'><span
    1163 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1472style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11641473mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
    1165 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11661475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    11671476parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
    1168 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11691478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
    1170 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1479<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11711480mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
    1172 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1481<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11731482mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
    1174 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1175 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
    1176 class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
    1177 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1178 mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
    1179 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1180 minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
    1181 check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
    1183 class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
    1184 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1185 minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
    1186 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1187 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
    1188 if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
    1189 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1190 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
    1191 I obtained an improved residual of ~9.05% with a much better fit at the high
    1192 angle part of the pattern but still not fit well for the lower part.</p>
     1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&amp;<b
     1485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>.
     1487The go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     1489Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span
     1490style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1491mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make the <b
     1492style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer
     1494radius</span></b> <b style='mso-bidi-font-weight:normal'><span
     1495style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1496mso-hansi-theme-font:minor-latin'>1000</span></b> if you didn’t do this earlier.
     1497Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1498mso-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
     1500much better fit at the high angle part of the pattern but still not fit well
     1501for the lower part.</p>
    11931502
    11941503<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12021511diffuse scattering feature at ~5deg and there are some peak shape issues (which
    12031512may be a consequence of the poor background fit). We’d like the fit to be
    1204 better before trying charge flipping. First select <span class=GramE><b
    1205 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1206 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span>
    1207 set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1513better before trying charge flipping. First select <b style='mso-bidi-font-weight:
     1514normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1515minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <b
     1516style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12081517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
    12091518background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1210 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1519style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12111520mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
    12121521window changes to </p>
     
    12211530
    12221531<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
    1223 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1224 mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
    1225 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1226 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
    1227 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1532style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1533mso-hansi-theme-font:minor-latin'>5.0</span></b> for <b style='mso-bidi-font-weight:
     1534normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1535minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>, <b
     1536style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12281537mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
    1229 for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1230 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1231 mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
    1232 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1538for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1539mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b>
     1540and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12331541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
    1234 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1542for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12351543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
    12361544(as appropriate for broad diffuse peaks) and then check all three refine boxes.
    1237 Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1238 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
    1239 class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></span>
    1240 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1241 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
    1242 for the <span class=SpellE>chebyschev</span> part of the background. The window
     1545Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1546mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
     1547pulldown 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:
     1549minor-latin'>5</span></b> for the chebyschev part of the background. The window
    12431550should look like</p>
    12441551
     
    12511558
    12521559<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
    1253 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1560style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12541561mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
    12551562tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1256 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1563"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    12571564minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1258 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1565style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12591566mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
    1260 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1567normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    12611568minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
    12621569the refinement converges. After a set of refinement cycles go to the <b
    1263 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b>
    1265 tab and check the intensities. If there are many negatives amongst the highest
    1266 angle reflections do <b style='mso-bidi-font-weight:normal'><span
    1267 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1268 mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all
    1269 the values with those in the extracted from the profile as listed in the <b
    1270 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1570style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
     1572reflections</span></b> tab and check the intensities. If there are many
     1573negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
     1574normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1575minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
     1576replaces all the values with those in the extracted from the profile as listed
     1577in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12711578mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    12721579list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
    12731580their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
    1274 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1581style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12751582mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
    1276 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1583style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12771584mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
    12781585vicinity of the reset ones</span>. You may repeat this process to suppress any
    12791586new negatives that may appear. Then set all the Pawley refinement flags back on
    12801587(excluding any that lead to a singular matrix) and repeat the refinement. After
    1281 refinement, mine converged to ~5.7% with very few negatives and <span
    1282 class=SpellE>and</span> the plot looked like</p>
     1588refinement, mine converged to ~5.7% with very few negatives and and the plot
     1589looked like</p>
    12831590
    12841591<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12941601
    12951602<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
    1296 Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1603Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12971604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
    12981605and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1299 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1606"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    13001607minor-latin'>Charge flip controls</span></b> in the middle of the <b
    1301 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1608style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13021609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    13031610tab.</p>
     
    13071614"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    13081615</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    1309 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1616style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13101617mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
    1311 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1618style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13121619mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
    1313162011bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
    13141621set to be used those in <b style='mso-bidi-font-weight:normal'><span
    1315 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1622style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13161623mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
    13171624data set; these should match the <b style='mso-bidi-font-weight:normal'><span
    1318 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1625style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13191626mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
    13201627
     
    13231630"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    13241631</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
    1325 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1632style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13261633mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
    1327 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13281635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
    13291636controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
    1330 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13311638mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
    13321639routine.</p>
    13331640
    13341641<p class=MsoNormal>For powder data it is not usually advisable to select a <b
    1335 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13361643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
    13371644element</span></b>; if selected a periodic table appears – select an element or
    1338 ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1645‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13391646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
    1340 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1647The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13411648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
    13421649defines the map spacing and thus the extent of the reflection set; the observed
    13431650reflection set is zero filled to this limit for charge flipping. The <b
    1344 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1651style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13451652mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
    1346 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1653and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13471654mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
    1348 determine the lower threshold and upper limit for charge flipping,
    1349 respectively. The latter is used to avoid “Uranium solutions” in the result.
    1350 Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1351 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1352 minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
    1353 ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
    1354 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1355 mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
    1356 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1655determine the lower threshold and upper limit for charge flipping, respectively.
     1656The latter is used to avoid “Uranium solutions” in the result. Set this to <b
     1657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>10-12</span></b>
     1659for equal atom problems and larger for heavy atom ones. For sucrose set it to <b
     1660style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1661mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>12.</span></b>
     1662When ready select <b style='mso-bidi-font-weight:normal'><span
     1663style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1664mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>; a
     1665progress bar dialog will appear that tracks the residual found in each charge
     1666flipping cycle. It will quickly drop to some level (42-44%) and then for a
     1667successful charge flipping run perhaps drop again into the 20-25% range after a
     1668considerable length of time. You should save the project if you get an
     1669apparently good solution. Many times it will not drop below ~40%; just try <b
     1670style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13571671mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
    1358 flipping</span></b>; a progress bar dialog will appear that tracks the residual
    1359 found in each charge flipping cycle. It will quickly drop to some level
    1360 (42-44%) and then for a successful charge flipping run perhaps drop again into
    1361 the 20-25% range after a considerable length of time. You should save the
    1362 project if you get an apparently good solution. Many times it will not drop
    1363 below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
    1364 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1365 mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
    1366 several tries fail to yield a solution, go back to the last step of the Pawley
    1367 refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
    1368 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1369 mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
    1370 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1371 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
    1372 This will generate a different set of intensities for the highly overlapped
    1373 part of the powder pattern; perhaps they will give a successful charge flip
    1374 solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
    1375 charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
    1376 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1377 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
    1378 to stop the charge flipping; a peak list and a drawing of the solution will
    1379 appear. One of my runs gave</p>
     1672flipping</span></b> again. If several tries fail to yield a solution, go back
     1673to the last step of the Pawley refinement and just repeat it (that is do <b
     1674style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1675mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
     1676update</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1677style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1678mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). This will
     1679generate a different set of intensities for the highly overlapped part of the
     1680powder pattern; perhaps they will give a successful charge flip solution.
     1681Unless 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:
     1683normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1684minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
     1685charge flipping; a peak list and a drawing of the solution will appear. One of
     1686my runs gave</p>
    13801687
    13811688<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14891796position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
    14901797width:16px;height:35px'><img width=16 height=35
    1491 src="Charge%20Flipping%20-%20sucrose_files/image052.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
     1798src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
    14921799style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
    14931800 o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
     
    14961803  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
    14971804</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
    1498 src="Charge%20Flipping%20-%20sucrose_files/image053.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1805src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
    14991806
    15001807<p class=MsoNormal>The result looks very promising! Charge flipping operates
     
    15031810flipping also will give a solution without regard to handedness; this solution
    15041811may be either the correct one for sucrose or its inverse.) Errors in these
    1505 phases can disrupt this process so that the map and peak positions are offset
    1506 from their true positions. To discover this and fix it, rotate the drawing
    1507 around to check that atom positions are related via the 2<sub>1</sub> screw
    1508 axis (through the multicolored cross in the center of the cell and parallel to
    1509 the y-axis – the green cell edge). Avoid motions with the right mouse button
    1510 pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
    1511 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1512 minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
    1513 cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
    1514 drawing above to show where I think it should be. If you find an offset to the
    1515 map, orient it so the offset is horizontal or vertical and then press the <b
    1516 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1812phases can disrupt this process so that the map and peak positions are offset from
     1813their true positions. To discover this and fix it, rotate the drawing around to
     1814check that atom positions are related via the 2<sub>1</sub> screw axis (through
     1815the multicolored cross in the center of the cell and parallel to the y-axis –
     1816the green cell edge). Avoid motions with the right mouse button pressed, this
     1817moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
     1818style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1819mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
     1820cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my drawing
     1821above to show where I think it should be. If you find an offset to the map,
     1822orient it so the offset is horizontal or vertical and then press the <b
     1823style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15171824mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
    1518 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1825<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15191826mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
    1520 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1827<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15211828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
    1522 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1829or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15231830mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
    15241831keys to shift the map and peaks as needed. The shift is in resolution units
     
    15361843  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
    15371844</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
    1538 src="Charge%20Flipping%20-%20sucrose_files/image054.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1845src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
    15391846
    15401847<h2>Step 4: Obtain solution from charge flip result</h2>
     
    15431850the map and make atoms out of them. The map peak list is initially sorted by
    15441851peak magnitude; you can change the sorting to be along any of the column
    1545 headings in the table by a single click on the desired heading. The <span
    1546 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1547 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1548 minor-latin'>dzero</span></b></span> column gives the distance of each peak from
    1549 the origin. The menu items under Map peaks give you several tools to aid in the
    1550 peak selection process; we will just use a couple in this example. I have
    1551 chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
    1552 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1553 mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
    1554 the unique ones. </p>
     1852headings in the table by a single click on the desired heading. The <b
     1853style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1854mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
     1855column gives the distance of each peak from the origin. The menu items under
     1856Map peaks give you several tools to aid in the peak selection process; we will
     1857just use a couple in this example. I have chosen to proceed by sorting the
     1858atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1859mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>,
     1860selecting all and then finding the unique ones. </p>
    15551861
    15561862<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    15581864"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    15591865</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
    1560 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1866normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    15611867minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
    15621868will sort the peaks in increasing z-axis coordinate.</p>
     
    15721878"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    15731879</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    1574 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1575 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should
    1576 select (grey) 23 out of 46 peak positions in the table and all should be near
    1577 the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
    1578 that would be all the C &amp; O atoms! They will be colored green in the plot.
    1579 If more are selected then check the map offset – it may need a slight
    1580 correction.</p>
     1880style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1881mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
     1882should select (grey) 23 out of 46 peak positions in the table and all should be
     1883near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
     1884that would be all the C &amp; O atoms! They will be colored green in the plot. If
     1885more are selected then check the map offset – it may need a slight correction.</p>
    15811886
    15821887<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15951900  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
    15961901</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
    1597 src="Charge%20Flipping%20-%20sucrose_files/image055.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1902src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    15981903
    15991904<p class=MsoNormal>Notice that in my case one atom is in a neighboring
    16001905molecule, one can deselect it and then pick the desired equivalent. Hold the <b
    1601 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1906style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16021907mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
    16031908key down and use the right mouse button to pick/unpick atoms in the drawing.
     
    16071912
    16081913<p class=MsoNormal>These are now ready to turn into atoms. Do <b
    1609 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1914style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16101915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
    16111916peaks/Move peaks</span></b>. The drawing will show white balls for each of the
    16121917selected positions and the <b style='mso-bidi-font-weight:normal'><span
    1613 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1918style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16141919mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
    16151920atoms. </p>
     
    16211926  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
    16221927</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
    1623 src="Charge%20Flipping%20-%20sucrose_files/image056.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
     1928src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
    16241929
    16251930<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16321937<p class=MsoNormal>The atom names indicate the peak magnitude to aid
    16331938identification (M100 for the largest in the <b style='mso-bidi-font-weight:
    1634 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1939normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16351940minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
    16361941may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
    1637 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1942style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16381943mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
    16391944them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
    1640 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16411946mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
    1642 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1947normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16431948minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
    16441949and then selecting a position in the table with the <b style='mso-bidi-font-weight:
    1645 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1950normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16461951minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
    16471952Linux machines the <b style='mso-bidi-font-weight:normal'><span
    1648 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1953style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16491954mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
    16501955the operating system; use <b style='mso-bidi-font-weight:normal'><span
    1651 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1652 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. After
    1653 sorting by magnitude, my list is now </p>
     1956style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1957mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
     1958After sorting by magnitude, my list is now </p>
    16541959
    16551960<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16651970of ambiguity in the middle, but just assign the top 11 as O and the rest as C
    16661971and see what happens. You can do this by selecting a block of atoms, go to <b
    1667 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1972style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16681973mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
    16691974atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
    1670 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1671 mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
    1672 periodic table will appear. Select the desired element and they will be changed
    1673 in the list and drawing.</p>
     1975style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1976mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a periodic
     1977table will appear. Select the desired element and they will be changed in the
     1978list and drawing.</p>
    16741979
    16751980<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16791984  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
    16801985</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
    1681 src="Charge%20Flipping%20-%20sucrose_files/image057.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
    1682 
    1683 <p class=MsoNormal>The original charge flipping solution is still visible and
    1684 the atoms are now identified, I’ve changed the drawing to show balls and sticks
    1685 and labeled the atoms with their names, this is done in the <b
    1686 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1687 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
    1688 tab. Double click the appropriate column heading and make the selection from
    1689 the dialog box.<span style='mso-spacerun:yes'>  </span></p>
     1986src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1987
     1988<p class=MsoNormal>The original charge flipping solution is still visible and the
     1989atoms are now identified, I’ve changed the drawing to show balls and sticks and
     1990labeled the atoms with their names, this is done in the <b style='mso-bidi-font-weight:
     1991normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1992minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b> tab. Double
     1993click the appropriate column heading and make the selection from the dialog
     1994box.<span style='mso-spacerun:yes'>  </span></p>
    16901995
    16911996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16972002
    16982003<p class=MsoNormal>Now one can safely remove the map peaks (do <b
    1699 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2004style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17002005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
    17012006peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    1702 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2007style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17032008mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
    1704 charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1705 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1706 mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
    1707 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1708 minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
    1709 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2009charge flip map (do <b style='mso-bidi-font-weight:normal'><span
     2010style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2011mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b
     2012style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17102013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    17112014tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
     
    17172020"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17182021</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    1719 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2022style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17202023mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
    1721 (hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2024(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17222025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
    17232026key down and select the appropriate rows). </p>
     
    17272030"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17282031</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    1729 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2032style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17302033mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
    17312034will appear at end of list and in the drawing. </p>
     
    17352038"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17362039</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
    1737 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2040normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    17382041minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
    17392042double click on upper left corner box of the table.</p>
     
    17432046"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17442047</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    1745 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2048style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17462049mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
    17472050will appear that are bonded to the molecule.</p>
     
    17522055</span></span></span><![endif]>Select these new atoms that are in the molecule;
    17532056they will probably be outside the unit cell box. Do this on the drawing with <b
    1754 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2057style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17552058mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
    17562059for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
    1757 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2060style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17582061mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
    17592062will show in green. </p>
     
    17632066"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17642067</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
    1765 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2068style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17662069mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
    1767 selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
    1768 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1769 minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
    1770 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1771 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
    1772 for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
    1773 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1774 mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
    1775 for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
    1776 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1777 minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
    1778 operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
    1779 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1780 minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
    1781 translations.</p>
     2070selections and make note of the <b style='mso-bidi-font-weight:normal'><span
     2071style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2072mso-hansi-theme-font:minor-latin'>Sym Op</span></b> for each one. In my case
     2073they were “<b style='mso-bidi-font-weight:normal'><span style='font-family:
     2074"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2075minor-latin'>2+1,0,0</span></b>” for O(4) and “<b style='mso-bidi-font-weight:
     2076normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2077minor-latin;mso-hansi-theme-font:minor-latin'>2+2,-1,1</span></b>” for O(3).
     2078The first number is the symmetry operator number and the 3 numbers after the ‘<b
     2079style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2080mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’
     2081are unit cell translations.</p>
    17822082
    17832083<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17852085"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17862086</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    1787 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2087style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17882088mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
    17892089
     
    17922092"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17932093</span></span></span><![endif]>Select an atom in turn that needs to be moved,
    1794 e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
     2094e.g. in my case O(3) or O(4). </p>
    17952095
    17962096<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17982098"Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17992099</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    1800 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1801 mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
    1802 style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
    1803 select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
    1804 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2100style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2101mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the
     2102operator and unit cell translations, then press <b style='mso-bidi-font-weight:
     2103normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18052104minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
    18062105coordinates will be transformed.</p>
     
    18132112
    18142113<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
    1815 with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight:
    1816 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1817 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>
    1818 to see the completed molecule. I’ve made it a balls &amp; sticks with names as
    1819 labels.</p>
     2114with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span
     2115style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2116mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
     2117completed molecule. I’ve made it a balls &amp; sticks with names as labels.</p>
    18202118
    18212119<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18252123  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
    18262124</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
    1827 src="Charge%20Flipping%20-%20sucrose_files/image058.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     2125src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    18282126
    18292127<p class=MsoNormal>Save the project file; the next step is to complete the
    1830 structure by finding H-atoms and then do the final <span class=SpellE>Rietveld</span>
    1831 refinements.</p>
     2128structure by finding H-atoms and then do the final Rietveld refinements.</p>
    18322129
    18332130<h2>Step 5: Complete the structure</h2>
    18342131
    18352132<p class=MsoNormal>To complete the structure you will need to perform a
    1836 preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
    1837 atom positions more accurate and prepare a set of calculated structure factors
    1838 needed to generate a difference Fourier map good enough to maybe reveal the H
    1839 atoms. There are a number of steps needed to set all the controls from the
    1840 previous Pawley refinement to get a successful start for the <span
    1841 class=SpellE>Rietveld</span> refinement.</p>
     2133preliminary Rietveld refinement. This will make the atom positions more
     2134accurate and prepare a set of calculated structure factors needed to generate a
     2135difference Fourier map good enough to maybe reveal the H atoms. There are a
     2136number of steps needed to set all the controls from the previous Pawley
     2137refinement to get a successful start for the Rietveld refinement.</p>
    18422138
    18432139<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18452141"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18462142</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    1847 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2143style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18482144mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
    18492145GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
    1850 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2146style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18512147mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
    18522148start with these when the scale factor is unknown.</p>
     
    18562152"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18572153</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
    1858 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18592155mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
    1860 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2156style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18612157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
    18622158scale factor</span></b> box. This is the scale factor for the data set. Uncheck
    1863 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1864 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
    1865 class=SpellE>displ</span></span></b>.</p>
     2159the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2160mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
     2161displ</span></b>.</p>
    18662162
    18672163<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18692165"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18702166</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
    1871 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2167style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18722168mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
    1873 uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2169uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18742170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
    18752171cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
    1876 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2172style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18772173mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
    18782174latter is most important; if you forget you will just get another Pawley
     
    18802176
    18812177<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
    1882 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2178style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18832179mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    1884 GSAS-II data tree menu; only scale and background are refined. I got <span
    1885 class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
    1886 intensity differences; the atom positions obviously need refinement.</p>
     2180GSAS-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
     2182need refinement.</p>
    18872183
    18882184<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18972193
    18982194<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
    1899 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2195style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19002196mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
    1901 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2197style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19022198mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
    19032199tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
    19042200has an arbitrary location along the y-axis. Then double click the <b
    1905 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2201style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19062202mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
    19072203column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
    1908 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2204normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19092205minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
    1910 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2206press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19112207mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    19122208The atoms table will show the refinement controls</p>
     
    19212217<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
    19222218y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
    1923 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2219style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19242220mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
    19252221data tree.</p>
     
    19332229
    19342230<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
    1935 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2231style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19362232mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
    1937 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1938 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
    1939 class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
    1940 fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
     2233style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2234mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0::dAy:0 for
     2235O(1)</span></b>’ from the dialog box. This will fix the shift along y for the
     2236O(1) atom.</p>
    19412237
    19422238<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19482244
    19492245<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
    1950 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2246style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19512247mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
    19522248show the hold</p>
     
    19602256
    19612257<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    1962 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1963 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
    1964 class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
    1965 parameters (in the <b style='mso-bidi-font-weight:normal'><span
    1966 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1967 mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
    1968 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2259mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is
     2260now ~10.3%. You can now safely refine lattice parameters (in the <b
     2261style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     2263tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19692264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
    1970 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2265the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19712266mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    19722267parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
    1973 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2268style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19742269mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
    1975 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2270normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19762271minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
    1977 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2272style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19782273mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
    1979 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2274<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19802275mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1981 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2276&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19822277mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    1983 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1984 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
    1985 class=SpellE>displ</span></span></b>. You can also include refinement of atom
    1986 thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
    1987 refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
    1988 map will show anything.<br>
    1989 Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2278and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
     2280displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>)
     2281parameters. My refinement improved slightly to Rwp~10.0%. Let’s see if a
     2282difference Fourier map will show anything.<br>
     2283Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19902284mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
    19912285General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
    1992 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1993 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
    1994 down the window.</p>
     2286style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2287mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway down
     2288the window.</p>
    19952289
    19962290<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    19972291mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    19982292"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1999 </span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
    2000 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2001 minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
    2002 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2003 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
    2004 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2293</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
     2294style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2295mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b
     2296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20052297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
    20062298
     
    20092301"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    20102302</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    2011 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2303style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20122304mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
    2013 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2305the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20142306mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    20152307set from</span></b> item (the only choice). The Fourier calculation will use
    20162308the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
    2017 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2309style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20182310mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
    20192311data set.</p>
     
    20232315"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    20242316</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    2025 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20262318mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
    2027 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2319style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20282320mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    20292321tab window. The map will be computed via fast Fourier techniques and is very
     
    20362328"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    20372329</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    2038 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2330style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20392331mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
    2040 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2332style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20412333mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
    20422334level</span></b> slider until something appears on the map. You can also reduce
    2043 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2335the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20442336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
    20452337to help clarify the view.</p>
     
    20512343  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
    20522344</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
    2053 src="Charge%20Flipping%20-%20sucrose_files/image059.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
    2054 
    2055 <p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
    2056 whose size are proportional to the electron density. There are peaks that might
    2057 be H-atom positions as well as features that suggest C &amp; O-atoms out of
    2058 position. Recall that the refinement was just done without any H-atoms; it will
    2059 make the best fit compensating for the missing H-atoms by displacing the C
    2060 &amp; O atoms in the direction of the missing H-atoms. </p>
     2345src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
     2346
     2347<p class=MsoNormal>What is drawn here are green dots whose size are
     2348proportional to the electron density. There are peaks that might be H-atom
     2349positions as well as features that suggest C &amp; O-atoms out of position.
     2350Recall that the refinement was just done without any H-atoms; it will make the
     2351best fit compensating for the missing H-atoms by displacing the C &amp; O atoms
     2352in the direction of the missing H-atoms. </p>
    20612353
    20622354<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20642356"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    20652357</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    2066 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2067 mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
    2068 style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</p>
     2358style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2359mso-hansi-theme-font:minor-latin'>Phases/sucrose<span
     2360style='mso-spacerun:yes'>  </span>Draw Atoms</span></b> tab.</p>
    20692361
    20702362<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20732365</span></span></span><![endif]>Select a C or O atom with possible H-atom
    20742366density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
    2075 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2367style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20762368mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
    20772369position the cross on the selected atom.</p>
     
    20842376with the left mouse button and shift the cross with the right mouse button. You
    20852377can zoom in using the roll wheel on the mouse (or else use the <b
    2086 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20872379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
    20882380distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
    2089 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20902382mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
    20912383lacks a wheel).</p>
     
    20972389  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
    20982390</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
    2099 src="Charge%20Flipping%20-%20sucrose_files/image060.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     2391src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    21002392
    21012393<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    21032395"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21042396</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
    2105 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2397normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    21062398minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
    21072399a white ball will appear at the selected position and an H-atom (name = <b
    2108 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2400style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21092401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
    21102402will be appended to the end of the atom list. Repeat steps 1-4 for as many
     
    21192411  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
    21202412</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
    2121 src="Charge%20Flipping%20-%20sucrose_files/image061.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
     2413src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
    21222414
    21232415<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    21252417"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21262418</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
    2127 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2419normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    21282420minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
    2129 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21302422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
    21312423they will be renamed and make then all ball &amp; stick. Do a <b
    2132 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21332425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2134 there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
    2135 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2136 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
    2137 map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    2138 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2139 mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
    2140 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2141 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
    2142 level</span></b> and <b style='mso-bidi-font-weight:normal'><span
    2143 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2144 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
    2145 the remaining H-atoms; you may have to guess positions for some of them using
    2146 known stereochemistry rules. My model looked like</p>
     2426there should be a drop in Rwp. Then repeat the <b style='mso-bidi-font-weight:
     2427normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2428minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> in
     2429the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2430mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     2431tab, 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:
     2433minor-latin'>Contour level</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2434style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2435mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the
     2436remaining H-atoms; you may have to guess positions for some of them using known
     2437stereochemistry rules. My model looked like</p>
    21472438
    21482439<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21522443  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
    21532444</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
    2154 src="Charge%20Flipping%20-%20sucrose_files/image062.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
     2445src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
    21552446
    21562447<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    2157 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2448style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21582449mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
    2159 stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
    2160 with all the H-atoms included (but not refined). The fit looks pretty good</p>
     2450stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms
     2451included (but not refined). The fit looks pretty good</p>
    21612452
    21622453<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21712462<p class=MsoNormal>Looking at the fit, there may be room for improvement and
    21722463we’d like to refine the H-atom positions. First we need to change the profile
    2173 model to include crystallite size and <span class=SpellE>mustrain</span>
    2174 broadening. Go to <b style='mso-bidi-font-weight:normal'><span
    2175 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2176 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
    2177 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2178 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    2179 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2180 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    2181 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2464model to include crystallite size and mustrain broadening. Go to <b
     2465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
     2467Parameters</span></b>, set <b style='mso-bidi-font-weight:normal'><span
     2468style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2469mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
     2470normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2471minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> to <b
     2472style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21822473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
    21832474and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2184 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2475"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    21852476minor-latin'>Refine</span></b> flags for them.</p>
    21862477
    21872478<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
    2188 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2479style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21892480mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
    2190 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2481style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21912482mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
    21922483tab; make sure the <b style='mso-bidi-font-weight:normal'><span
    2193 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2484style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21942485mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
    2195 boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2196 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2197 mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
    2198 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2199 minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
    2200 and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2201 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2202 mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
     2486boxes 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:
     2488minor-latin'>Cryst. size</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2490mso-hansi-theme-font:minor-latin'>microstrain</span></b>.</p>
    22032491
    22042492<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22102498
    22112499<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    2212 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2213 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    2214 class=SpellE>Rwp</span> will start out high but should converge to where it was
    2215 before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
    2216 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2217 mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
     2500style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2501mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
     2502start out high but should converge to where it was before this change. I got
     25038.08% 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:
     2505minor-latin'>Data tab</span></b> looked like</p>
    22182506
    22192507<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22252513
    22262514<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
    2227 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2228 mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
    2229 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    2230 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2231 minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
    2232 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2233 mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
    2234 phenomenological model for <span class=SpellE>microstrain</span> which has 9
    2235 terms for monoclinic structures. Check all the boxes for it.</p>
     2515style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2516mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <b
     2517style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2518mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain
     2519model</span></b>; this is the Stephens phenomenological model for microstrain
     2520which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
    22362521
    22372522<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22432528
    22442529<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    2245 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2246 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    2247 class=SpellE>Rwp</span> will start out high but should converge lower than
    2248 where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
    2249 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2250 minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
    2251 If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2252 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2253 mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
    2254 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2255 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
    2256 type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
    2257 surface plot for ground sucrose.</p>
     2530style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2531mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
     2532start out high but should converge lower than where it was before this change.
     2533I got 7.65% and the <b style='mso-bidi-font-weight:normal'><span
     2534style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2535mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. If you check
     2536the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2537mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain</span></b>
     2538button 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:
     2540minor-latin'>Select plot type</span></b> box, you will see the interesting
     2541mustrain surface plot for ground sucrose.</p>
    22582542
    22592543<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22652549
    22662550<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    2267 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2551style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    22682552mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    22692553 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     
    22752559<p class=MsoNormal>Before refining H-atom positions it would be wise to create
    22762560restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
    2277 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2561normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    22782562minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
    22792563GSAS-II data tree; there will be an almost blank window telling you there are
    22802564no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
    2281 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2282 mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
    2283 style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
    2284 a dialog box will appear asking for the origin atom for the bond. </p>
     2565style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2566mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
     2567will appear asking for the origin atom for the bond. </p>
    22852568
    22862569<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22922575
    22932576<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    2294 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2577style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    22952578mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
    2296 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2579style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22972580mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    22982581A new dialog box will appear asking for the target atoms for the bonds.</p>
     
    23062589
    23072590<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    2308 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23092592mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
    2310 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2593normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23112594minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
    23122595dialog box appears asking for the bond length</p>
     
    23212604
    23222605<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
    2323 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2606style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23242607mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
    2325 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2608style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23262609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    23272610I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
    2328 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2611the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23292612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
    2330 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2613to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23312614mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
    23322615and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2333 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2616"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    23342617minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
    23352618and H-O bond lengths.</p>
     
    23432626
    23442627<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
    2345 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2628style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23462629mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
    23472630there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
    2348 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2631style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23492632mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
    23502633will appear asking for the A atom in the angle A-B-C. Select <b
    2351 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23522635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
    23532636The next dialog asks for the B atom in the A-B-C angle, select <b
    2354 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2637style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23552638mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
    2356 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2639and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23572640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
    23582641The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
    2359 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2642normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23602643minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
    23612644tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
    2362 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23632646mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
    23642647they are listed in order of the B atom. O-atoms should have one angle apiece;
     
    23732656
    23742657<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
    2375 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2658style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23762659mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
    2377 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2660normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23782661minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
    2379 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2662<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23802663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
    23812664from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
    2382 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2665normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23832666minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
    2384 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2667style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23852668mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
    23862669atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
    2387 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2670style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23882671mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
    23892672for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
    2390 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2673style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23912674mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
    2392 list progress on the “Penalty function” (i.e. the restraints) and the <span
    2393 class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
    2394 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2395 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
    2396 weight factors</span></b> to tighten them up at some expense in <span
    2397 class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
    2398 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2675list progress on the “Penalty function” (i.e. the restraints) and the Rwp drops
     2676in my case to ~7.05%. One can increase the <b style='mso-bidi-font-weight:normal'><span
     2677style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2678mso-hansi-theme-font:minor-latin'>Restraint weight factors</span></b> to
     2679tighten them up at some expense in Rwp. In the end I chose <b style='mso-bidi-font-weight:
     2680normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23992681minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
    2400 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24012683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
    2402 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2684and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24032685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
    2404 restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
    2405 positions may not be correct even though the refinement apparently succeeded.
    2406 You should check that the OH ones all give reasonable H-bonds to neighboring
    2407 O-atoms. As this is powder data such changes will hardly affect the fit but
    2408 will be more satisfying. At present such checking is outside the scope of
    2409 GSAS-II.</p>
     2686restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be
     2687correct even though the refinement apparently succeeded. You should check that
     2688the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is
     2689powder data such changes will hardly affect the fit but will be more
     2690satisfying. At present such checking is outside the scope of GSAS-II.</p>
    24102691
    24112692<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • Tutorials/CFsucrose/Charge Flipping - sucrose_files/filelist.xml

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