Friday, 14 October 2016

Scaling data processed with DIALS in SADABS

The chemical crystallography community like "sadabs" for scaling, so we have added the ability to export data in a format which sadabs can consume (strictly: this is an ersatz EvalCCD format.) Essentially following integration with DIALS (e.g. with xia2 or otherwise) run:

dials.export 1_integrated_experiments.json 1_integrated.pickle \
    sadabs.hklout=int1.sad run=1 format=sadabs
...
dials.export 2_integrated_experiments.json 2_integrated.pickle \
    sadabs.hklout=int2.sad run=2 format=sadabs

where you have runs 1...N in your data set (typical for small molecule crystallography work). You can then run sadabs as you usually would, and should see something like:

 Reading file int1.sad
 Reading file int2.sad
 Reading file int3.sad
 Reading file int4.sad

 Mean and maximum errors in direction cosine check function =   0.000   0.000
 The mean error should not exceed 0.005, and is usually caused by matrix
 changes during data processing.

 Approximate wavelength, cell and maximum 2-theta (from cosines etc.):
 0.69010    5.432    8.147   12.053   89.994   90.026   90.002   72.46

in the output, showing in this case that the answers were about as expected. 

Your mileage may vary, this has just been implemented, you will also want the output from:

dials.two_theta_refine p4p=sad.p4p 1_integrated_experiments.json 1_integrated.pickle ...

with the pickle files and json files above to get the unit cell and error for subsequent analysis. Took this data through sadabs, xprep, shelxt, shelxl and the answers seemed sensible...

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