# Changeset 870

Ignore:
Timestamp:
Mar 21, 2013 11:13:48 AM (10 years ago)
Message:

fix plot

File:
1 edited

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Removed
• ## trunk/help/Charge Flipping - sucrose.htm

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Step 4 Obtain solution from charge flip result

class=SpellE>dzero column gives the distance of each peak from the origin. The menu items under Map peaks give you several tools to aid in the peak selection process; we will just use a couple in this example. I have chosen to proceed by sorting the atoms by z, selecting all and then finding the unique ones.

minor-latin'>dzero column gives the distance of each peak from the origin. The menu items under Map peaks give you several tools to aid in the peak selection process; we will just use a couple in this example. I have chosen to proceed by sorting the atoms by z, selecting all and then finding the unique ones.

Map peaks/Unique peaks. That should select (grey) 23 out of 46 peak positions in the table and all should be near the top of the list. Given the formula for sucrose is C12H22O11 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks. That should select (grey) 23 out of 46 peak positions in the table and all should be near the top of the list. Given the formula for sucrose is C12H22O11 that would be all the C & O atoms! They will be colored green in the plot. If more are selected then check the map offset  it may need a slight

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The drawing shows the selected atoms in green.

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Notice that in my case one atom is in a neighboring

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Notice that in this case the atom list is neatly sorted out into two groups with a clear gap between M79 and M64. The higher ones are likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of ambiguity in the middle, but just assign the top 11 as O and the rest as C and see what happens. You can do this by selecting a block of atoms, go to

Notice that in this case the atom list is neatly sorted out into two groups with a clear gap between M79 and M64. The higher ones are likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of ambiguity in the middle, but just assign the top 11 as O and the rest as C and see what happens. You can do this by selecting a block of atoms, go to Edit/Modify

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The original charge flipping solution is still visible and

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Interestingly the atoms identified exactly matched with the mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General tab). The atom positions I obtained have two atoms (O3 & O4) not connected to the sucrose molecule because they belong to neighboring molecules. We need to discover the equivalent ones that belong to this molecule. Follow the steps:

to the sucrose molecule because they belong to neighboring molecules. We need to discover the equivalent ones that belong to this molecule. Follow the steps:

Draw Atoms table by a double click on upper left corner box of the table.

minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms table by a double click on upper left corner box of the table.

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Save the project file; the next step is to do  the Rietveld class=GramE>do  the Rietveld refinement on the completed structure.

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Ive shifted & zoomed in to make the differences more

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To deal with the warning we need to set a Hold on one atom

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Do an Reflection set from item (the only choice). The Fourier calculation will use the structure factors shown in the item (the only choice). The Fourier calculation will use the structure factors shown in the Reflection list item for this PWDR be H-atom positions as well as features that suggest C & O-atoms out of position. Recall that the refinement was just done without any H-atoms; it will make the best fit compensating for the missing H-atoms by displacing the C &O atoms in the direction of the missing H-atoms.

make the best fit compensating for the missing H-atoms by displacing the C &O atoms in the direction of the missing H-atoms.

Phases/sucrose  Draw Atoms tab.

mso-hansi-theme-font:minor-latin'>Phases/sucrose  Draw Atoms tab.

General tab, adjust the Contour level and Map radius as desired. Look for the remaining H-atoms; you may have to guess positions for some of them using known stereochemistry rules. My model looked like

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour level and Map radius as desired. Look for the remaining H-atoms; you may have to guess positions for some of them using known stereochemistry rules. My model looked like

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Calculate/Refine, the console will list progress on the Penalty function (i.e. the restraints) and the Rwp drops in my case to ~7.05%. One can increase the Restraint weight factors to tighten them up at some expense in Rwp. In the end I chose 2.0 for both Restraint weight factors to tighten them up at some expense in Rwp. In the end I chose 2.0 for both Bond and

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