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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Quickly Generating a Slant Plane Difference Fourier Electron Density Contour Map on an Atom of Interest

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[Tutorials page] | [WinGX Tutorial Index]

The Fourier Map generator and Viewer in WinGX is one of the main Killer Applications of this software suite in allowing powerful routine aid in structure solution and quality checking of the structure. (It should be noted that software such as Sir97, CRYSTALS, EXPO, GSAS and Platon also generate Fourier Contour Maps, but WinGX (and Platon?) is potentially the most accessible and convenient for non-Shelx generated structures to use) While optimised for working with Shelx, any application that can generate a Shelx *.ins structure file and a *.fcf (H K L Fobs, Fcalc) file can make use of this Fourier Viewing feature. The trick here is to use an OMIT command on the atom of internet combined with a LIST 3 command. Shelx generates an FCF file when using the LIST 3 command. WinGX generates the entire MAP file (which takes longer) but then allows people to quickly browse through the map, and also use its ANIMATE function to automatically scroll through the slices.

The following example is based on Cs Ti Silicate where one of the oxygens (O13) has a very large thermal and a warning in Ton Speks platon as well as visual inspection warranted closer inspection.

In WinGX, edit the Shelx INS file, set the L.S. (least squares) to 0 cycles; OMIT the atom(s) of interest (so they show up in the difference map); and make sure there is a LIST 3 command to generate the FCF file which allows a Fourier Map to be derived calculated.
L.S.  0

For the following inorganic (polymeric) structure. If the atom of interest is not well placed to get the desired 3 atom slant plane, you can use the graphical viewing in such programs as Cameron combined with the WinGX Model, Operations, Assemble Residues to get the atom of interest centred. We will generate a slant plane using O12, O13 and O10 to define the plane.

  • view of the structure with Cameron

    Now run Shelx under the Refine menu option.

  • After running Shelx, go into the Maps, Fourier Map, browse and select the 3 atoms (O12, O13 and O10) that make up the slant plane.
  • Selecting Atoms that make up the Plane

  • Set the Zmin and Zmax to -2 and +2 so you can get a decent slice through Z. You can set the range of the map to anything you like.
  • Setting the range of the Fourier Map

  • Now select OK to generate the Map. This make take a few minutes depending on the size of the map

  • Generating the Fourier Map

  • Map Generation Completed

    Select Dismiss to exit the Fourier Map generator.

  • Now select Maps, Contour to view the Fourier Map. And go into Options, Label Atoms and select the (O12, O13 and O10) atoms.

  • Viewing the Fourier Map, selecting
Atom labels

  • Then you can select the start movie option until you find the view of interest. In the following case, you can see the slight Peanut shape of the Oxygen implying a split atom problem for this Oxygen.

  • Viewing a slightly disordered Oxygen

  • Other Options exist for viewing Fourier maps in WinGX such as using mapview for various 2D and 3D display options.

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