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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Analytical Face Index Absorption Correction

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [WinGX Tutorial Index]
[Pro's and cons of Analytical vs Gaussian Face Index Absorption Correction]

This example uses the raw hkl data used to determine the crystal structure of Cs2TiSi6O15 as published in I.E. Grey, R.S. Roth, M.L. Balmer, Journal of Solid State Chemistry, 131, 38-42 (1997).

The starting information that is normally known before starting WinGX is:

  • Wavelength of radiation used.
    • 0.71073 Angstrom (Mo K-alpha)
  • Space group
    • C2/c
  • Unit Cell Dimensions:
    • a=13.3860(0.002) b=7.4230(0.002) c=15.1340(0.001) beta=107.710(0.05)
  • Cell contents/Composition:
    • Cs2TiSi6O15
    • Z (number of formula units in the cell) =4 (WinGX can try to estimate Z)
  • 2-theta scan range
    • 2 to 30
  • Colour and habit of crystals
    • colorless, transparent tabular-shaped crystals.
  • Crystal size
    • 0.24mm x 0.24mm x 0.10mm
  • Absorption Correction: Analytical using crystal faces (distances in mm) 
    CELL    13.385   7.422  15.133  90.00 107.70  90.00
FACE      2   0   0   0.12000
FACE     -2   0   0   0.12000
FACE      0   2   0   0.12000
FACE      0  -2   0   0.12000
FACE      0   0   2   0.05200
FACE      0   0  -2   0.05200

At this point we have already defined the space group and wish to do a Face Index Absorption Correction. This assumes you have an HKL file with direction cosines. Run WinGX to bring up the following Menu Bar

Starting Menu Bar

Click on Absorb, Numerical, Analytical menu option to enter the absorption correction option.

Going into the absorption correction option

If WinGX detects an existing faces.def file, which has the indices and distance information, (implying you this is not the first absorption correction you have attempted on this sample) it will query whether you want to use this.

Query to use existing faces.def file

The faces.def file has the following format (distances in mm) 

CELL    13.385   7.422  15.133  90.00 107.70  90.00
FACE     2   0   0   0.12000
FACE    -2   0   0   0.12000
FACE     0   2   0   0.12000
FACE     0  -2   0   0.12000
FACE     0   0   2   0.05200
FACE     0   0  -2   0.05200

If you already have kosher a faces.def file to use, just used this, other wise refer to XtalView and Entering Faces for the First Time which will show you how to enter the faces via the WinGX GUI menu.
If using an existing faces.def file, one thing you may like to do is go into XtalView and just check that the crystal does look like the original one mounted on the diffractometer. Cancel out of the absorption correction and run Absorp, Numerical, Xtal View and examine what the crystal looks like.

XtalView Screen

After exiting XtalView, go back to the procedure and tell WinGX you do want to use the existing faces.def file.

WinGX will leave a Platon Dialog Window where you can check a summary.

Platon Text Dialog Window

After removing the Platon summary screen, WinGX will leave a confirmation dialog box stating how it has created a new HKL file with the absorption corrected intensities.

WinGX confirm dialog box

The thorough Platon output is in the absorb.lst file where you can check the exact corrections Platon has performed on your HKL data. This can be accessed easily via the top menu under Analyse, Open List File, ABSORP

   H   K   L       F**2     Sig(F**2)     Transmission      Volume (mm3)
   0   0 -20      845.92       30.71         0.43737        0.00628806759
   0   2 -19      110.40       15.49         0.42736        0.00628806759
  -1   1 -19      192.97       18.52         0.43188        0.00628806759
  -4   0 -18      397.35       18.86         0.42851        0.00628806759
The new Shelx ready absorption corrected hkl file is titled analytcl.hkl. You can rename you cosine based hkl file with direction cosines to a backup file then copy the analytcl.hkl file to be the project hkl file that will be used for solution and/or refinement. Though for refinement, WinGX can detect what types of HKL files you have allowing you to vary the type of absorption corrected HKL files you are using so you can explore the effect of absorption on the structure.

WinGX asking what HKL file you want to use for Shelx

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