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:
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
Click on Absorb, Numerical, Gaussian menu option to enter 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.
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.
Enter each face index one at a time, pressing the Enter Face
Button after each input.
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.
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.
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.
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.