In this module diffraction intensities are normalized using the Wilson method. Statistical analysis of the intensities is made in order to suggest the presence or absence of the inversion center, to identify the possible presence and type of pseudotranslational symmetry (Cascarano et al. 1988 a,b; Fan, Yao et al. 1988) and to detect preferred orientation effects (Altomare et al. 1994; Altomare et al. 1996). Possible deviations (of displacive type) from ideal pseudotranslational symmetry are also detected. All the above information is used as prior information in the integrated intensities extraction process, unless the directive NOPSEUDO is given to the program.
When some additional prior information, besides positivity and atomicity of electron density, is available, then a suitable renormalization of structure factors is made.
Directives in normal command
The following directives must be added after the command '%normal' in the input file to activate some specific features of the procedure
BFACTOR x
Temperature factor if the user wants to supply it. (The scale factor is assumed equal to 1).
NOPREFERRED
If this directive is given the program does not apply the correction for preferred orientation.
NOPSEUDO
If this directive is given the program does not recycle the PSEUDO information in a new extraction process.
NREFLECTIONS n
Number of active reflections with largest E-values subject to a minimum value of E(obs) = 1.0.
Default = 4 * number of independent atoms + 50 if centrosymmetric + 50 if triclinic + 150 to a maximum of 499. If PSEUDO directive is on, the program tries to use all the E's down to 1.0.
NZRO n
Number of smallest E-values (maximum E-value 0.3) to calculate psi-zero triplets. The default (and the maximum) is 1/3 of the strong reflections. (The directive allows to decrease that number).
NPLA n
n is the number of candidate planes for preferred orientation analysis (default 10; maximum 30)
The number includes the equivalent planes which will not be considered.
PLANE h k l G
Preferred orientation direction supplied by the user; G is the correction factor.
PSEUDOTRANSLATION n(1,1) n(2,1) n(3,1) n(4,1) n(1,2) . . . n(4,3)
If parameters are equal to zero, or omitted, the normalization routine performs statistics for the pseudotraslation effects and renormalizes the reflections on assuming the most probable pseudotranslation as prior information.
If user wants to supply a specific pseudotranslational symmetry, and this corresponds to a class given in Table 1 the n(1,1) can be set to the class number and the other values must be omitted.
If the pseudotranslation is more complex, it should be specified by up to 3 sets of 4 values n(i,j) so that
( n(1,j)*h + n(2,j)*k +n(3,j)*l = n(4,j)*m ) j=1,..,3
where m is an integer number.
THRP x
Threshold value of the mean fractionary scattering power (M.F.S.P.) to recycle the pseudo-translational symmetry information in a new extraction process.
Example
Example 1
Use of the pseudotranslational symmetry (if it is present) as prior information for a new extraction process is inhibited.
%structure agpz
%job AGPZ - data from home diffractometer
%initialize
%data
pattern agpz.pow
cell 6.526 20.059 6.464 90.000 90.000 90.000
spacegroup p b c a
content Ag 8 N 16 C 24 H 24
wavelength 1.54056
filetype xy
%extraction
%normal
nopseudo
%continue
References |
Cascarano G., Giacovazzo C. & Luic' M. (1988a). Acta Cryst. A44, 176-183.
Cascarano G., Giacovazzo C. & Luic' M. (1988b). Acta Cryst. A44, 183-188
Fan H., Yao J. & Qian J. (1988). Acta Cryst. A44, 688-691.
Altomare A., Burla M.C., Cascarano G., Giacovazzo C., Guagliardi A., Moliterni, A.G.G. & Polidori, G. (1996). J. Appl. Cryst. 29, 341-345.
Altomare A., Cascarano G., Giacovazzo C., Guagliardi A., Burla M.C., Polidori G. & Camalli M. (1994). J. Appl. Cryst. 27, 435 - 436.
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