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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Defining the Faces for the First time - and Viewing with XtalView

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, Gaussian 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, 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

It is actually easier to edit the faces.def file manually, especially if you have a lot of indices defining the crystal. However for this exercise, we will do this via the menu system which can be quite tedious if you have a lot of faces. Thus we will not use the existing faces.def file. WinGX then prompts with the following Window for you to enter the faces.

Menu input for face information

Enter each face index one at a time, pressing the Enter Face Button after each input.

Menu input for face information

Enter OK to complete the input; after which WinGX will Prompt whether you want to view the crystal you have described using XtalView. Say yes will allow you to confirm that the crystal you have input matches the crystal you have physically mounted.

XtalView Prompt

XtalView Screen

After exiting XtalView, WinGX will automatically start Platon. Be patient here as Platon is crunching away performing the absorption correction, it just isn't giving much indication of it. Depending on the nuances of the version of Platonyou may or may not see the Platon graphics screen. Presently the graphics screen will be bypassed and will go straight to the Platon dialog window.

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. 

  H  K  L  TRANSM    MU*T   INTENSITY  SIGMA    I(COR)
================================================================================
  0  0-20 0.44011   0.8207       370     31       841
  0  2-19 0.43028   0.8433        47     15       110
 -1  1-19 0.43423   0.8342        83     18       192
 -4  0-18 0.43139   0.8408       170     19       395
 -2  0-18 0.42822   0.8481       777     31      1815
  0  0-18 0.42001   0.8675        55     29       130
 -1  1-18 0.42423   0.8575        18     16        43
 -3  1-18 0.43035   0.8431       220     20       511
 -4  2-18 0.43158   0.8403       157     19       365
The new Shelx ready absorption corrected hkl file is titled gaussian.hkl. You can rename you cosine based hkl file with direction cosines to a backup file then copy the gaussian.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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