leonarski_fandFilip Leonarski
19b135186d
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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Symmetry evidence
Independent space-group assessments, by POINTLESS and ZANUDA, of the open-arm sets whose symmetry
rugnux and the deposition disagree about, plus the sets the twin review flagged. They are there to
decide which answers the battery accepts, not to judge the depositions. An exact pseudo-symmetry,
a twin or another special effect can produce any of these results. How they are made: the
"Symmetry evidence" section of ../README.md. Battery rows as scored in run 20261012-0139
(rc175 fcbe920), before any change these results may prompt.
| set | deposition | rugnux | battery row | what the programs found |
|---|---|---|---|---|
| 6oww | P 1 21 1 | P 41 21 2 | fail (sym_over) | ZANUDA prefers P 43 21 2 over P 21 on all four data sets, with lower R-free each time. |
| 6toc | P 42 | P 42 2 2 | pass (accepted_alternative) | Open: ZANUDA prefers P 42 2 2 on every data set; R-free does not agree between free sets. |
| 6pxb | P 32 | P 31 1 2 | pass (accepted_alternative) | ZANUDA keeps the deposited P 32 on every data set; P 32 1 2 with the deposited model refines far worse. |
| 8xte | P 32 | P 31 2 1 | pass (accepted_alternative) | ZANUDA keeps the deposited P 32: the deposited model does not obey the two-fold P 32 2 1 adds. |
| 8xtg | P 32 | P 31 2 1 | pass (accepted_alternative) | Open: ZANUDA prefers P 32 2 1 on every data set; R-free favours P 32 on every one. |
| 3r6o | I 41 | I 41 2 2 | fail (sym_over) | The deposited I 41 is supported; the deposited model gives I 41 2 2 no support. |
| 4bwl | P 1 21 1 | C 2 2 21 | fail (sym_over) | The deposited P 21 with a near-perfect twin is supported; the deposited model gives C 2 2 21 no support. |
| 2wnq | P 1 21 1 | C 2 2 21 | fail (sym_over) | The deposited P 21 with a near-perfect twin is supported; the deposited model gives C 2 2 21 no support. |
| 5ebi | P 1 21 1 | C 2 2 21 | fail (sym_over) | ZANUDA cannot judge this set: its refinement does not reproduce the deposited fit. |
| 8c3e | P 31 2 1 | P 6 2 2 | fail (sym_over) | The deposited P 31 2 1 is supported; the deposited model gives a 622 group no support. |
| 6p8j | P 1 21 1 | P 1 21 1 | pass | rugnux and the deposition agree (P 21); ZANUDA rejects the orthorhombic group POINTLESS suggests. |
| 5cc8 | P 21 21 2 | P 21 21 21 | fail (sym_screw) | The depositor's axial reflections support the deposited P 21 21 2; our own axial reflections do not settle the screw. |
| 9hnc | P 1 2 1 | P 1 21 1 | fail (sym_screw) | The depositor's axial reflections support the deposited P 2 (no screw along b); in both data sets odd-order reflections are weak along every axis, so absence statistics favour P 21 without deciding it. |
| 5ky6 | P 1 21 1 | P 1 2 1 | fail (sym_screw) | The deposited P 21 is supported; rugnux's P 2 has no support in its own data, which measure only five 0k0 reflections, all at noise level. |
| 7k1l | P 63 | P 6 | unscored (screw_undetermined) | No data set decides the screw along c; the row's "unscored, screw undetermined" is consistent with this. |
| 7mzt | P 21 21 2 | P 21 21 21 | unscored (screw_undetermined) | No data set decides the screw along c; the row's "unscored, screw undetermined" is right. |
| 7orr | I 21 3 | I 2 3 | pass | The intensities cannot separate I 2 3 from I 21 3, as the battery already scores it; the deposited model (I 21 3) is consistent. |
| 8s38 | I 21 21 21 | I 2 2 2 | pass | The intensities cannot separate I 2 2 2 from I 21 21 21, as the battery already scores it; the deposited model (I 21 21 21) is consistent. |
Not examined: 2ygz (no deposited model; the entry is withdrawn and the set has left the open arm) and 9rci (its accepted alternative is a cell, P 1 in a doubled cell, not a symmetry question).