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Tutorials and Examples

CRYSTALS Single Crystal Suite

Using DIFABS in Crystals as a diagnostic test

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

Why bother using DIFABS Analysis?

"You can use DIFABS in test mode at any stage, and it quite simple tells you if there is a systematic trend to the residual as a function of orientation. If the plot is fairly monochrome, then the residuals are not peaking up. If there are bright patches, it means that there is a systematic trend to the residual. Either FO or Fc is systematically wrong. Possible reasons are:

  • Absorption
  • crystal damage (bending, shearing)
  • anisotropic extinction
  • mis-centering
  • very anisotropic 'spot' shape (selective truncation)
  • Application of unsuitable/ill-measured psi correction
    (Use of DIFABS in 'test' mode to un-corrected and psi-corrected data can help display the effect of the correction more clearly than just looking at Rint)
  • We have no evidence that missing atoms (eg solvent) lead to Difabs-like effect"

To use DIFABS for diagnosis of your structure, from the main menu use Analysis, Difabs analysis

Running Difabs analysis via Crystals

Output from an inorganic Cesium Titanium Silicate after the final stages of refinement

Contour plot output from a DIFABS analysis in Crystals 

R-value=  3.906                                   Rw=  7.074                   
 (Sum Fo)/(Sum Fc)=   1.00 Minimisation function=       1959.                   
                                                                                
 There are    0 singularities                                                   
 Sum of the squares of the ratio (Shift/e.s.d.)  =          0.0000              
 The rms (shift/esd) =        0.000464                                          
 The rms (shift/esd) is less than the target (  0.300000 ).                     
 Futher cycles abandoned                                                        
 Largest shift/esd (=  0.002275), for Parameter   101 O     12 U[23]            
 Statistics for   112 least squares parameters, with  1762 degrees of freedom   
                                      X-rays        Restraints         All      
 Number of observations               1874               0            1874      
 Hamilton weighted R-value           7.074           0.000           7.074      
 !                             

1360 #SCRIPT XDIFABS                                                           
 This SCRIPT runs DISABS in test mode. Use the SCRIPT DIFABS                    
 to apply the correction.                                                       
 DIFABS Version  9.01 Applied to Fo or Fc                                       
 There is no orientation matrix.                                                
 DIFABS correction will not be optimal                                          
               0            Processing reflections            100%              
       DIFABS correction applied to Fo                                          
               0            Processing reflections            100%              
 For the  1764 reflections                                                      
 the relative residual was 0.0343   and the relative rms residual was 0.0363    
                                                                                
  1874 Reflections corrected. Average correction = 0.998 (On Fo)                
   Minimum correction = 0.958 Maximum correction = 1.088

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