v1.0.0-rc.184 #95
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Reference: mx/Jungfraujoch#95
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The detector-frame surfaces are held to a mean of one within each resolution shell, because a factor that is a function of d alone is a null direction of their fit. That mean was weighted by 1/sigma^2, and sigma is smallest where little light arrives: on a detector part-shadowed by the pin the dark cells carry the shell's mean, and their large factors go onto the lit cells as small ones. How much of a ring is shadowed varies with resolution, so this bends the merged intensities along resolution: REFMAC's fitted scale against the model ran 1.48 / 0.80 / 1.16 in F (1.65 A / 2.7 A / inner) on a half-shadowed lysozyme sweep, with R as good as XDS's within every shell and 0.02 worse over all, and no shell-wise statistic can see it. Each observation now counts once. REFMAC R-work / R-free on the depositor's flags (d_min of the baseline), model as deposited, 31 sets chosen by the largest removed ramp and clamped cells, largest R vs per-shell R gap, plus controls: 5 better by more than 0.0015, 23 the same, 3 worse. half-shadowed lysozyme 0.3266 / 0.3306 -> 0.2996 / 0.3069 (XDS on the same model 0.3036 / 0.3083) soft X-ray insulin 0.2720 / 0.2841 -> 0.2423 / 0.2570 4p8r 0.2143 / 0.2518 -> 0.1873 / 0.2216 (depositor's data 0.2216) 6i3j -0.0029; insulin reference -0.0017; 2wnz +0.0025, 6jgh +0.0016, 5j23 +0.0015. The ramp removed on the first falls from 186x to 2x. The merge's own hash test records change as they must. A mean over the ring still lowers its lit part by the shadow it averages in (the new test reads 0.72 where 0.57 before and 1 would be exact); a median of the counts did not do better on the half-shadowed sweep (R-free 0.3090), the only one it was measured on. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HVeDQs733XDnbQQyUbV1vsWith modules x images at or above what the card's HBM holds for the internal frame generator (64 module frames in the HLS simulation, 1024 on the card), frame_generator refuses the run and sends nothing, and the collection hung in Measuring with no error. The host now checks this: PrepareAction refuses such a run at the start (a 32-bit EIGER frame counts twice, as in frame_generator.cpp), and SetInternalGeneratorFrame refuses an image that would land there, each with an error that says how many module frames fit. The capacity comes from hbm_size_bytes of the card's status (the mock keeps its 64). The check keeps the last module frame free as well: load_calibration.cpp accepts module_id == 2 * hbm_size_bytes / module size (">" where ">=" was meant), one past the memory. The firmware is frozen, so the host never sends that index instead. The HLS simulation keeps frame_generator's return code: a refused configuration cancels the data collection rather than waiting for frames, and HLSSimulatedDevice::FPGA_EndAction throws with the code. rc184 has no MockAcquisitionDevice: its part is left out, and the test checks HLSSimulatedDevice only, as HLSSimulatedDevice_InternalGeneratorMemory in FPGAIntegrationTest. (ported from rc184-225542a9af) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAKA model of several chains is searched for as a whole and then, side by side, as one chain of each molecule in it (chains with the same residue at every number they share are one molecule; the most complete one is searched), with the PAE domains' machinery. The whole model's choice stands unless a chain's search chose a placement better by the R-free margin (0.03), or the whole model chose none; the chains that chose must agree on the space group. MR_SEARCH_MODEL names the winner ("chain A, one of 2 alike"). An experimental dimer from another crystal form, placed as one rigid unit where the target crystal holds the two copies at another separation (tNCS), was placed 3.4 A off per chain (R-free 0.47); the chain search places both copies (R-free 0.28 before refinement, refined 0.27), and where the dimer is right the whole model is kept (R-free 0.26 against the chain's 0.29). MR takes about twice as long on such a model (0.55 -> 1.1 s). With tNCS by half a lattice vector, the placement and its moves by (v + o)/2 are now told apart by a paired per-reflection test of |F_obs - F_calc| on the weak reflections (3 standard errors, as the equal-copies group comparison) instead of a 0.01 margin in R over them; UNDECIDED only where the best is not ahead of every other by that. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK (cherry picked from commit 690ee4784ddd8e046fec19edb558f28808d0a825)A frame whose background region reads below zero - a detector module whose pedestal is off on that frame - integrates reflections with a negative background variance, a sigma floored at one photon and a net intensity of thousands (I/sigma ~8000). The unscaled merge the per-image scales are fitted against weights such an observation ~100x above any real one, so it takes its reflection over; every frame that sees that reflection and finds nothing there is then pulled towards a scale of 0 (the proportional model error caps such an observation's normalised residual at ~3.3 sigma, so the Cauchy fit never rejects it and its pull grows as G falls), lands under the 1/50 floor and is dropped, and the partiality refit against the survivors drops more. On a serial run whose detector shows this on one module every 324th frame, always on the same residue of the frame number modulo 4, two same-arm quarters of the run (frames mod 4 = 0 and = 2) merged to CC1/2 0.78 and 0.28. The collapsed frames were good frames (CC with the deposited model's Fcalc 0.29 against 0.34 for the kept ones, the same hand) whose CC with the scaling reference was 0.03: the reference, not the frames, was wrong. Measured (frames mod 4 = 0 / = 2, run's geometry): before: 446 / 1355 frames dropped, R_split 32.6 / 64.0%, <I^2>/<I>^2 2.08 / 2.74, <|L|> 0.475 / 0.788, CC of the merge with the model Fcalc (d >= 2.5 A) 0.842 / 0.381 after: 446 / 412 dropped, R_split 32.6 / 35.9%, 2.08 / 2.17, 0.475 / 0.478, 0.842 / 0.816 The whole run: 9081 -> 3081 frames dropped, CC1/2 0.59 -> 0.955, R_split 18.6 -> 14.9%, Fcalc CC 0.879 -> 0.884 (d >= 2.5 A); two runs without the defect are unchanged. AcceptReflection now refuses such an observation (a NaN variance, from older files, is kept), so it leaves every stills scale fit, merge and ambiguity correlation, and the stills merge logs how many observations on how many frames were left out. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK (cherry picked from commit bd5c59915fd7698afcc0ef81722e562c78c5ee3a)