leonarski_fandClaude Fable 5.1
7782e304ed
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The refinement's density calculators (the CPU engine's, the GPU engine's and the map gradient's) cut every atom's density at an absolute 1e-4 e/A^3 of its blurred density instead of gemmi's default 1e-5. The radius, the gather's box and the gradient's box all follow from it, so the structure factors, the gradients and with them the refined model change in the last digits. Molecular replacement's and the validation's own calculators keep gemmi's default. Where this sits against other programs' defaults, which are relative to the atom's own peak density: cctbx resolves phenix.refine's wing_cutoff to 1e-3 of the peak below 5 A (1e-4 above), X-PLOR's ELIM 7 is e^-7 of the peak and SFALL's VDWR 2.5 about 2e-3 of it. For carbon at B + blur of 20-120 A^2 an absolute 1e-4 is 6e-5 to 6e-4 of the peak - still stricter than any of them. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu