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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Absorption Correction Using DIFABS

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [WinGX Tutorial Index]

Before using DIFABS, it is suggested that you read the following journal article:
  • Nigel Walker and David Stuart, "An Empirical Method for Correcting Diffractometer Data for Absorption Effects", Acta Cryst. (1983), A39, 158-166.
DIFABS has received a larged amount of bad verbage as a practical method ("DIFABS is EVIL!"). How much of this is based in reality, paranoia, philosophy, etc is still up for discussion(?). It is possible for DIFABS to be used to soak up sloppy practises in diffractometer setup and crystal alignment (non-full irradiation of the crystal), etc, etc, etc.

A web page to refer to is "Should DIFABS be Banned?":

Within the limitations described in the original DIFABS paper above, it does seem(?) to be a method worth keeping in your crystallographic bag of tricks to get the job done under some circumstances. Anyway, one of the brilliant advantages of WinGX is that it does let you easily test out a variety of absorption correction methods for yourself. (It should be repeated that for many of these methods, WinGX uses the facilities within Ton Spek's Platon [CCP14 Web Mirror]. This is available for UNIX, DOS and Windows). It should also be noted that for any other crystallographic software to access this wide variety of absorption correction methods, one easy way to do this is just make your software "Platon Friendly". This also gives you the ability to access a wide variety of analytical algorithms inside Platon.

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 DIFABS 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

While the face information is available, DIFABS would normally be used if this information did not exist. Though it is possible that DIFABS could be used on top of face index absorption corrected data to tweak the absorption(?)

A solved crystal structure where major atoms are refined isotropically and no extinction or similar corrections have been applied. The following structure solved with DIRDIF PATTY and refined on Shelx93 are given. 

CS1     2   0.11731   0.24153   0.41000  11.00000   0.03096
TI1     4   0.25000   0.25000   0.00000  10.50000   0.01342
SI1     3  -0.00258   0.23084  -0.14685  11.00000   0.01192
SI2     3   0.32391   0.42925  -0.16631  11.00000   0.01826
SI3     3   0.34547   0.04062  -0.14463  11.00000   0.02011
O1      1   0.38138   0.23869  -0.17005  11.00000   0.03024
O2      1   0.30201   0.05003  -0.05699  11.00000   0.02313
O3      1   0.10762   0.18887  -0.07442  11.00000   0.02694
O4      1   0.24671   0.45812  -0.27011  11.00000   0.04433
O5      1   0.00000   0.23843  -0.25000  10.50000   0.07003
O6      1   0.26365   0.42388  -0.09048  11.00000   0.02687
O7      1  -0.08560   0.07390  -0.14348  11.00000   0.05764
O8      1  -0.04847   0.41752  -0.12658  11.00000   0.04985
At this point we have solved the structure, refined the atoms isotropically and wish to apply DIFABS to generate the absorption corrected data. This assumes you have an Unmerged HKL file with direction cosines. Run WinGX to bring up the following Menu Bar

Starting Menu Bar

Click on Absorb, RefDelF, DIFABS, General menu option to enter the Difabs absorption correction option.

Going into the absorption correction option

WinGX will pass this over to Platon, where it will generate a output window (as shown below). WinGX may also quickly bring up then quit a Platon absorption surface plot.

Platon Text Output Window

After removing the Platon summary screen, WinGX will leave a confirmation dialog box stating .

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

  1975 Reflections corrected (Corrections on F**2)
Min. absorption corr. = 0.378 for  -16   0  -4  at  Phi(P)= 176.4 Mu(P)=   4.2   Phi(S)= 298.9 Mu(S)=   4.2
Max. absorption corr. = 2.103 for    0   0  -2  at  PHI(P)=  89.8 MU(P)=   0.0   PHI(S)= 264.1 MU(S)=   0.0
Average absorption correction = 1.017
 
Minimum, Maximum Virtual Transmission:  0.101 0.564
 
***VALUES FOR COEFFICIENTS***
 
    0.6365   -0.0138    0.0010    0.2830    0.0040    0.0010
   -0.2128   -0.0685    0.2126    0.0774   -0.0081   -0.0134
 
    0.4841    0.1398   -0.0280   -0.1501
   -0.0016   -0.0183   -0.0097    0.1744
 
   -0.1732   -0.0187   -0.0024   -0.3789    0.0258   -0.0014    0.0599
    0.4957    0.0355   -0.2192    0.0344   -0.0450    0.0860   -0.0889
 
   -0.7614   -0.3010   -0.1200   -0.0308   -0.0602
    0.1350    0.2162    0.3040    0.1385   -0.6506
 
 
 
 
Absorption Surface for PHI =   0 ---> 170 WITH MU RANGE =  0 ---> 30
       0   10   20   30   40   50   60   70   80   90  100  110  120  130  140  150  160  170
  30  1.49 1.63 1.75 1.83 1.85 1.84 1.87 1.94 2.01 2.03 1.95 1.78 1.60 1.43 1.30 1.17 1.03 0.90
  25  1.53 1.68 1.80 1.87 1.87 1.85 1.88 1.96 2.06 2.10 2.02 1.85 1.63 1.43 1.26 1.11 0.97 0.84
  20  1.58 1.74 1.87 1.93 1.91 1.89 1.91 2.00 2.12 2.17 2.11 1.92 1.68 1.45 1.25 1.07 0.92 0.79
  15  1.65 1.82 1.95 2.00 1.98 1.95 1.97 2.06 2.20 2.27 2.22 2.02 1.76 1.49 1.26 1.05 0.88 0.74
  10  1.73 1.92 2.06 2.11 2.09 2.05 2.07 2.17 2.31 2.40 2.35 2.15 1.86 1.56 1.29 1.06 0.86 0.71
   5  1.84 2.03 2.18 2.25 2.24 2.21 2.24 2.35 2.49 2.58 2.51 2.30 2.00 1.67 1.37 1.10 0.87 0.69
   0  2.05 2.20 2.32 2.41 2.48 2.56 2.69 2.86 2.99 2.99 2.82 2.51 2.17 1.85 1.55 1.26 0.98 0.72
The new Shelx ready absorption corrected hkl file is titled difabs_g.hkl. You can rename you cosine based hkl file with direction cosines to a backup file then copy the difabs_g.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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