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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
62 lines
3.3 KiB
Bash
Executable File
62 lines
3.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Manually build the viewer inside one of the build-environment images and inspect its runtime .so
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# deps -- the quick way to confirm the static-libdbus + glib-off changes actually dropped the
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# dbus/systemd/glib/selinux tail. Defaults to the rocky9 image built by build_images.sh.
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#
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# The repo is mounted read-write at /workspace, but the CMake build tree lives in the container's
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# /tmp (thrown away with --rm), so nothing root-owned is left in your working copy. Building needs
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# network (FetchContent pulls curl/zstd/hdf5/...) but NOT a GPU.
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#
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# Usage:
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# docker/build_in_rocky9.sh # build viewer in jfjoch_rocky9:$TAG, then ldd it
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# docker/build_in_rocky9.sh rocky8 # use a different variant's image
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# TAG=2607b docker/build_in_rocky9.sh
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set -euo pipefail
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REGISTRY="${REGISTRY:-gitea.psi.ch/leonarski_f}"
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TAG="${TAG:-2607b}"
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VARIANT="${1:-rocky9}"
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IMG="$REGISTRY/jfjoch_$VARIANT:$TAG"
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repo="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" # repo root = docker/..
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echo "==> image $IMG"
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echo "==> repo $repo (mounted at /workspace; build tree in container /tmp)"
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docker run --rm \
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-v "$repo":/workspace -w /workspace \
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"$IMG" bash -lc '
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set -eux
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git config --global --add safe.directory /workspace || true
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# If this image predates the CMAKE_PREFIX_PATH fix, point cmake at the static libdbus config
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# dir so the viewer (Qt6::DBus -> find_package(DBus1)) resolves WrapDBus1. Harmless once the
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# image ENV already carries it.
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dbus_dir=$(ls -d /opt/dbus-*-static/lib/cmake/DBus1 2>/dev/null | head -1)
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cmake -G Ninja -S /workspace -B /tmp/build \
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-DJFJOCH_VIEWER_ONLY=ON -DJFJOCH_USE_CUDA=ON \
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${dbus_dir:+-DDBus1_DIR=$dbus_dir} \
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_CXX_FLAGS="-march=x86-64-v3" -DCMAKE_C_FLAGS="-march=x86-64-v3"
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ninja -C /tmp/build -j"$(nproc)" jfjoch_viewer
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bin=/tmp/build/viewer/jfjoch_viewer
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echo "===================== ldd jfjoch_viewer ====================="
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ldd "$bin" | sort
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echo "========== dbus/systemd tail (what the static libdbus removes) =========="
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# These only ever entered via the system libdbus-1.so -> libsystemd chain, so they MUST be gone.
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tail_re="libdbus-1|libsystemd|libzstd|liblz4|libgcrypt|libgpg-error|libcap\."
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if ldd "$bin" | grep -Ei "$tail_re"; then
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echo ">>> FAIL: the dbus/systemd tail is still linked"
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else
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echo ">>> OK: libdbus/libsystemd/zstd/lz4/cap/gcrypt/gpg-error all gone"
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fi
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echo "========== residual glib/selinux (expected on RHEL9, NOT from us) =========="
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# libglib here is pulled by the system harfbuzz/fontconfig/freetype text stack (glib-linked on
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# RHEL9), not by Qt -- QT_FEATURE_glib=OFF is honoured (Qt is off the glib event loop) but cannot
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# drop the font-stack glib. libselinux/libpcre2-8 come from the krb5/GSSAPI stack that static
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# curl links for auth (kept for the reverse-proxy Kerberos plan) -- same bucket as libcrypto.
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# Shedding these would mean static-linking the whole font stack / dropping krb5. (libpcre2-16 is
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# Qt-owned and legitimately stays.)
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ldd "$bin" | grep -Ei "libglib|gthread|selinux|libpcre\.|libpcre2-8" || echo "(none)"
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'
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