v1.0.0-rc.179 (#90)

* Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast.
* Rugnux: Stills can be indexed without a GPU, with a CPU implementation of the fast-feedback indexer (macOS, computers without a GPU).
* Rugnux: Rotation and stills data are integrated in the detector's own units with one gain model, improving data from CCD detectors.
* Web frontend: The Rugnux live page shows the placed model with its electron density and anomalous difference map in a Mol* viewer.

Reviewed-on: #90
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

image_analysis/structure_refinement/ModelValidation.cpp

@@ -21,6 +21,7 @@
 #include <string>
 #include <utility>
 #include <vector>
+#include <limits>
 #include <unordered_map>
 
 #include <gemmi/assembly.hpp>   // expand_ncs
@@ -1725,6 +1726,8 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
     // thrown away unread: they are not made at all.
     const bool maps_superseded = schedule.maps_superseded && schedule.maps_superseded(result);
     std::shared_ptr<ModelMaps> maps;
+    // The anomalous difference map's coefficients, where the merge kept the Bijvoet split: for the maps file too.
+    gemmi::AsuData<std::complex<float>> mapanom;
 
     if (!maps_superseded) {
         maps = std::make_shared<ModelMaps>();
@@ -1739,8 +1742,7 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
         // rather than leaving a list of coordinates for someone to look up.
         // Following ANODE, Thorn & Sheldrick (2011) J. Appl. Cryst. 44, 1285-1287
         std::future<void> anomalous_map = std::async(std::launch::async, [&] {
-            gemmi::AsuData<std::complex<float>> mapanom =
-                    anomalous_coefficients(merged, data_space_group != nullptr ? data_space_group : sg,
+            mapanom = anomalous_coefficients(merged, data_space_group != nullptr ? data_space_group : sg,
                                            result.indexing_op, fmodel);
             result.anomalous_pairs = static_cast<int>(mapanom.v.size());
             if (!mapanom.v.empty()) {
@@ -1809,6 +1811,11 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
                                                          {"FREE", 'I'}};
         for (const auto &[label, type] : columns)
             mtz.columns.push_back({label, type, type == 'H' ? 0 : 1, {}});
+        // The anomalous difference map's coefficients (ANOM/PHANOM, as phenix.maps names them), on the reflections
+        // that have a Bijvoet pair; missing (NaN) on the others.
+        std::unordered_map<long, std::complex<float>> anom_by_hkl;
+        for (const auto &hv : mapanom.v)
+            anom_by_hkl[hkl_key(hv.hkl)] = hv.value;
         for (size_t i = 0; i < terms.size(); i++) {
             // [0, 360), the convention the MTZ 'P' columns carried before sigma_A weighting: std::arg
             // returns (-180, 180] and a P column is not supposed to.
@@ -1825,6 +1832,18 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
             for (size_t c = 0; c < mtz.columns.size(); c++)
                 mtz.columns[c].values.push_back(row[c]);
         }
+        if (!anom_by_hkl.empty()) {
+            MtzTable::Column anom{"ANOM", 'F', 1, {}}, phanom{"PHANOM", 'P', 1, {}};
+            for (const auto &t : terms) {
+                const auto it = anom_by_hkl.find(hkl_key(t.hkl));
+                const float nan = std::numeric_limits<float>::quiet_NaN();
+                const double phi = it == anom_by_hkl.end() ? 0.0 : std::arg(it->second) * 180.0 / PI;
+                anom.values.push_back(it == anom_by_hkl.end() ? nan : std::abs(it->second));
+                phanom.values.push_back(it == anom_by_hkl.end() ? nan : static_cast<float>(phi < 0 ? phi + 360.0 : phi));
+            }
+            mtz.columns.push_back(std::move(anom));
+            mtz.columns.push_back(std::move(phanom));
+        }
     }
 
     result.ok = true;