Space group determination

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Space group determination by  EXPO2014

       In the crystal structure solution process the determination of the space group usually follows the indexing step. This task is carried out by a careful investigation of the experimental intensities, aimed at finding the correct extinction group. Because of the collapse of the experimental data into the Bragg angle one-dimension space, the experimental pattern suffers by peak overlap and uncertain background definition. As a consequence, the judge about the ‘presence’ or ‘absence’ of the reflections may provide ambiguous results. A new probabilistic procedure aiming at recognizing the extinction symbol has been implemented in  EXPO2014. It uses the statistics of the normalized z intensities (as extracted by the Le Bail method) to calculate the probability of each extinction symbol compatible with the crystal system suggested by N-TREOR09. A suitable weight w is associated to the intensity of each reflection, depending on the expected reliability of its estimate. The algorithm provides a probability for each extinction symbol of the considered crystal system. It has been tested on a large number of test structures and on all the crystal systems, providing good results (Altomare et al., 2004; Altomare et. al., 2005; Altomare et al., 2007). 


Preparing input file for space group determination by  EXPO2014

Space group determination by EXPO2013
Output of space group determination
Contact and References


Preparing input file for space group determination in  EXPO2014

       To run  EXPO2014 for space group determination you need to create an input file (*.exp). You can create an input file for space group determination by graphic interface by the menu "File" > "New".

You must specify the structure name, the profile counts filename and its format, the type of radiation source. Click on button 'Find Space Group', fill the frame 'Cell Parameters' and 'Cell Content'. The following picture is an example of input file for the crystal structure determination in case of cimetidine structure from the indexed pattern.

Once the button 'Save' has been selected, an input file cime.exp will be created and automatically loaded by the program for the space group determination.

%structure cime
%job structure cime
%init
%data
       pattern cime.pow
       filetype counts
       wave 1.52904
       findspace
       cell 10.69808 18.81786 6.82267 90.00000 111.28911 90.00000
       cont  h 64 c 40 n 24 s 4

%continue

       The directive findspace enables the space group determination procedure. It is a directive of the command %data. The unit cell is assumed to be determined by indexing of the experimental pattern. To know the meaning of the other lines of the input file, see the chapter "command and their use" of this manual. 

Alternatively you can edit a new input file or modify an exiting input file by a text editor and save it with extension '.exp'. Once a time the input file has been created, load the exp input file from menu 'File' > 'Load & Go'.



Space group determination by EXPO2013

The different steps of the algorithm are here schematized.
1) The full pattern decomposition is performed, according to the Le Bail algorithm, in the space group having the largest Laue symmetry and no extinction conditions (e.g., P 1 2/m 1 in the monoclinic system, P 2/m 2/m 2/m for the orthorhombic, P 4/m mm for the tetragonal, P 6/m mm for the trigonal-hexagonal, Pm-3m for the cubic systems).
2) The extracted intensities are then normalized, according to the classical Wilson method, by using the space group mentioned at the point 1).
3) The z statistic is used to define the probability of the extinction symbol.
4) For each crystal system the probability of the different possible extinction symbols is calculated.
Use the button on the toolbar to carry out to next steps.

At the end of the procedure the following window will be displayed.



The window contains the extinction symbols ranked according to their calculated probability. When the user clicks on one of them, the corresponding list of compatible space groups is supplied. The frequency of the selected space group in the Cambridge Structural Database (CSD) is reported in terms of number of occurrences in the CSD and percentage. This information can be useful when different space groups are associated to an extinction group.
Press the button  to access to a list of reflections that, according to the selected extinction symbol, should be systematically absent. For each reflection the following specifications are given: the order number of reflection, the Miller index, the symmetry operator responsible for the extinction and the corresponding extinction condition, the probability for the extinction, the type of reflection (single or in overlap).
By default the reflections are ordered according to the extinction condition but you can change the order selecting a different ordering criterion by clicking on the title column. The selected reflection on a list will be marked on the pattern.

The reflections that are expected to be absent according to the selected extinction symbol are marked by a vertical bars situated below the observed pattern, just above the set of bars defining the reflection positions. They have different colors depending on whether the reflection is single (or belongs to a whole extinct cluster) or in overlapping. By default, a black vertical bar marks single systematically absent reflections, while the rest of the absent reflections (those in overlap) are marked with  a purple bar. This graphical support helps the user to discard unreliable extinction symbols even if estimated with large probability.

Press the 'OK' button to accept the selected space group and continue with the structure solution process.



Output of space group determination

       The output file contains details about the space group determination procedure. Use 'Info' > 'View output file' to access to the output file or open the file structure_name.out with a text editor. At the end of the procedure the new input file, called structure_name1.exp (e.g. cime1.exp) will be created. This file contains the selected space group and can be loaded for skip the space group determination and to perform the structure solution with Direct Methods.

Contact

For suggestions and bugs contact angela.altomare@ic.cnr.it, annagrazia.moliterni@ic.cnr.itrosanna.rizzi@ic.cnr.itcorrado.cuocci@ic.cnr.it.


References

Altomare, A., Caliandro, R., Camalli, M., Cuocci, C., da Silva,  I., Giacovazzo, C., Moliterni, A. G. G. Spagna, R. (2004). Space-group determination from powder diffraction data: a probabilistic approach. J. Appl. Cryst. 37, 957-966.

Altomare, A., Camalli, M., Cuocci, C., da Silva, I. Giacovazzo, C., Moliterni, A. G. G Rizzi, R. (2005). Space group determination: improvements in EXPO2004. J. Appl. Cryst. 38, 760-767.

Altomare, A., Camalli, M., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G. and Rizzi, R. (2007). Advances

in space-group determination from powder diffraction data. J. Appl. Cryst. 40, 743-748.

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