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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Structure Solution Using Dirdif - Auto-Patty

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This example assumes you have done the determination of the space group using WinGX in a previous tutorial page..

In this tutorial/run-through, only a very minor portion of the functionality of Dirdif using the automatic structure solving PATTY mode. Dirdif, amongst other things, has excellent options for expanding structures and solving on fragments using Patterson search.

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) 
    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 Now we wish to try and solve this inorganic phase using Dirdif in automatic Patterson mode. If not already open, run WinGX to bring up the following Menu Bar

Starting Menu Bar

  • From the menu, select Files, Job Paths, Move Working Directory and select the root file (hkl or ins) from which you are going to work with.

    Selecting file/project to use

    		•
    Click on Solve, Dirdif, PATTY menu option to start to try and automatically solve the structure using Dirdif automatic Patterson methods.

    About to run Dirdif

    Dirdif then run and try and solve the structure.

    Dirdif runs

    When dirdif finishes, use File, Exit to exit the program in a civilised fashion. Dirdif has also output a Shelx *.res file.

    Dirdif has finished

    With Dirdif having now run, you can then enter Cameron or another graphics program of your choice; or examine the output file. In this case, it suggests the following trial structure solution for you to check out.

    TITL XYZN file = SHELXL INS file, from DIRDIF output for EG1SCR
CELL   0.71073   13.38600  7.42300 15.13400  90.0000 107.7100  90.0000
ZERR     4.000    0.00200  0.00200  0.00100   0.0010   0.0500   0.0500
LATT  +7
SYMM     -X   ,     Y   , 1/2-Z
SFAC      CS   O    SI   TI
UNIT      8   60   24    4
L.S.  3
REM      use BOND for distances and angles:
BOND
REM      FMAP 3 = electr.dens.,    FMAP 2:  Fo-Fc Fourier
FMAP  3
REM      Plan  n: print n additional Fourier peaks
REM      Plan -n: print includes connectivity
PLAN  -10
REM      TEMP nn = Temperature of data collect. in Celcius
REM      TEMP 20
REM      SIZE = crystal size in mm :
REM      SIZE 0.5 0.5 0.5
REM      crystal color and shape ?
REM      Write atoms file in PDB format (with H) :
WPDB  -1
REM      Warning: check HKLF below !!
REM      ----------------------------
REM      3=Fobs, 4=FobsSQ, > HKL file
FVAR     0.33670
CS1     1   0.11670   0.24067   0.40880  11.00000   0.02140
TI2     4   0.25000   0.25000   0.00000  11.00000   0.02140
SI3     3  -0.00071   0.23252  -0.14460  11.00000   0.02140
SI4     3   0.17671  -0.06959  -0.33149  11.00000   0.02140
SI5     3   0.34454   0.03862  -0.14244  11.00000   0.02140
O6      2   0.25164  -0.03664  -0.23045  11.00000   0.02140
O7      2   0.10899   0.19671  -0.07455  11.00000   0.02140
O8      2   0.38048   0.23630  -0.17128  11.00000   0.02140
O9      2   0.29954   0.05392  -0.06000  11.00000   0.02140
O10     2   0.23714   0.07285   0.09110  11.00000   0.02140
O11     2  -0.04929   0.41947  -0.12644  11.00000   0.02140
O12     2   0.00000   0.26946  -0.25000  11.00000   0.02140
O13     2  -0.08424   0.06798  -0.14176  11.00000   0.02140
HKLF    4
END

    Resulting Structure in Cameron

    Resulting Structure in Cameron

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