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dials.scale: should stop if incompatible input #2234

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graeme-winter opened this issue Sep 29, 2022 · 2 comments · May be fixed by #2526
Open

dials.scale: should stop if incompatible input #2234

graeme-winter opened this issue Sep 29, 2022 · 2 comments · May be fixed by #2526
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@jbeilstenedmands

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@graeme-winter
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cs04r-sc-com18-01 well_65 :) $ dials.show symmetrized.expt | grep "Unit cell"
    Unit cell: 110.396, 90.300, 110.342, 90.000, 90.005, 90.000
    Unit cell: 110.372, 90.250, 110.319, 90.000, 90.015, 90.000
    Unit cell: 78.140, 90.430, 78.143, 90.000, 89.994, 90.000
    Unit cell: 110.394, 90.249, 110.351, 90.000, 89.987, 90.000
    Unit cell: 110.241, 90.155, 110.228, 90.000, 89.991, 90.000
    Unit cell: 110.255, 90.158, 110.194, 90.000, 89.980, 90.000
    Unit cell: 78.082, 90.330, 78.029, 90.000, 90.148, 90.000
    Unit cell: 110.323, 90.303, 110.364, 90.000, 90.033, 90.000
    Unit cell: 109.868, 89.880, 110.011, 90.000, 89.970, 90.000
    Unit cell: 110.421, 90.267, 110.387, 90.000, 90.023, 90.000
    Unit cell: 110.395, 90.257, 110.369, 90.000, 89.974, 90.000
    Unit cell: 110.473, 90.269, 110.355, 90.000, 89.977, 90.000
    Unit cell: 110.377, 90.250, 110.295, 90.000, 90.022, 90.000
    Unit cell: 110.004, 89.990, 110.092, 90.000, 90.050, 90.000
    Unit cell: 110.329, 90.210, 110.291, 90.000, 90.008, 90.000

Output of dials.cosym job (which itself should raise alarm bells)

dials.scale does not crash


            -------------Summary of merging statistics--------------           

                                            Suggested   Low    High  Overall
High resolution limit                           2.10    5.71    2.10    1.40
Low resolution limit                          110.29  110.45    2.14  110.29
Completeness                                   99.9    99.2   100.0    80.5
Multiplicity                                   13.5    13.1    13.4     8.6
I/sigma                                        10.1    36.6     1.0     3.8
Rmerge(I)                                     0.982   0.231   7.133   1.593
Rmerge(I+/-)                                  0.977   0.229   7.096   1.572
Rmeas(I)                                      1.017   0.240   7.394   1.680
Rmeas(I+/-)                                   1.051   0.246   7.664   1.732
Rpim(I)                                       0.260   0.062   1.915   0.501
Rpim(I+/-)                                    0.379   0.088   2.823   0.696
CC half                                       0.992   0.992   0.208   0.648
Anomalous completeness                         99.5    99.1    99.7    66.8
Anomalous multiplicity                          6.9     6.9     6.8     4.8
Anomalous correlation                        -0.006  -0.078   0.018  -0.002
Anomalous slope                               0.784                        
dF/F                                          0.113                        
dI/s(dI)                                      0.687                        
Total observations                          1697276   83907   84284 2923062
Total unique                                 125389    6408    6294  339513

However dials.symmetry on scaled output swears loudly

Selected 208074 scaled reflections
Removed 57 intensity.scale.value reflections with I/Sig(I) < -5
Incompatible unit cell: 
      median unit cell:
@graeme-winter
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<- currently very 🤔 because cosym should have cleaned all this anyway?

jbeilstenedmands added a commit that referenced this issue Oct 18, 2023
@jbeilstenedmands
Add check for compatible cells in cosym output. Fixes #2234
f5d2a73
@jbeilstenedmands jbeilstenedmands linked a pull request Oct 18, 2023 that will close this issue
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@jbeilstenedmands
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My opinion is that this will become a non-issue when we have fixed the upstream cosym issues. dials.scale currently does not know anything about relative length and angle tolerances which would be needed to make such a check. I think if data has been suitably prepared by symmetry/cosym then we don't require further checks here.

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Add check for compatible cells in cosym output dials/dials
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@graeme-winter @jbeilstenedmands