paper_plots: R-free figure from the refined protocol on the shared free set by default

The R-free figure now draws refmac_refined_rfree_shared(_depdata): the deposited model refined
against each data set at its own resolution, R-free over the depositor's free reflections both data
sets share. --rfree first-cycle keeps the previous first-cycle rigid-body pair at the common
resolution. With the rechecked hq-pool3 runs the figure covers 160 structures (was 135).

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C

tools/battery/README.md

@@ -509,10 +509,11 @@ whole range; the manifest keeps the rule used as `dmin_rule`.
 
 ## Figures for publication
 
-`paper_plots.py RUN [RUN-REDO ...] --out DIR [--time-runs RUN ...] [--uncontended RUN]` draws three
-open-arm figures from a run's `results.json`: R-free of the deposited model after the REFMAC check
-(`--model-check`) on the depositor's data against Rugnux's data (same model, protocol, resolution
-and the depositor's free set), the deposited high-resolution limit against Rugnux's cut, and a
+`paper_plots.py RUN [RUN-REDO ...] --out DIR [--time-runs RUN ...] [--uncontended RUN] [--rfree refined|first-cycle]`
+draws three open-arm figures from a run's `results.json`: R-free of the deposited model after the REFMAC
+check (`--model-check`) on the depositor's data against Rugnux's data (by default the refined protocol:
+each data set at its own resolution, R-free on the shared free set; `--rfree first-cycle` for the
+first-cycle numbers at the common resolution), the deposited high-resolution limit against Rugnux's cut, and a
 histogram of the processing time per dataset with the median marked. Later runs fill in sets an
 earlier one did not run (a `-redo`). `--time-runs` takes the time histogram from other runs - one
 whose sets had the GPU to themselves - and `summary.txt` lists the provenance of both. Beside the PDF/PNG figures it writes the

tools/battery/paper_plots.py

@@ -15,9 +15,11 @@ statistics), figures.gp (the gnuplot script) and the rendered figures: a single-
 with embedded fonts and the same figure as a 600 d.p.i. PNG. gnuplot and pdftoppm (poppler) must be
 on PATH; gemmi reads the facility and beamline from each entry's cached mmCIF (_diffrn_source).
 
-Left figure: R-free of the deposited model after the battery's REFMAC check (model_check.py: the
-same model, protocol, resolution and the depositor's free set) on the depositor's data (x) and on
-Rugnux's data (y). Right figure: the deposited high-resolution limit (x) against Rugnux's own cut
+Left figure: R-free of the deposited model after the battery's REFMAC check on the depositor's data
+(x) and on Rugnux's data (y). By default the refined protocol (model_check.py: the same model
+refined against each data set at its own resolution, R-free over the free reflections both data sets
+share); --rfree first-cycle draws the first-cycle rigid-body numbers at the common resolution instead.
+Right figure: the deposited high-resolution limit (x) against Rugnux's own cut
 (y), log axes so the low-resolution entries show. Small molecules (no deposited model) and sets
 whose verdict is `fail` (a wrong lattice: nothing to compare) are left out.
 
@@ -67,7 +69,7 @@ set style line 1 lc rgb "black" lw 1.5 dt 2
 set style line 2 pt 7 ps 0.35 lc rgb "#0072b2"
 # counts: names left-aligned, numbers right-aligned in a column beside them
 set label 11 "Structures\nFacilities\nBeamlines" at graph 0.05, graph 0.93 left front
-set label 12 "%(n)d\n%(nf)d\n%(nb)d" at graph 0.36, graph 0.93 right front
+set label 12 "%(n)d\n%(nf)d\n%(nb)d" at graph 0.31, graph 0.93 right front
 
 # --- R-free
 set output "%(out)s/rfree.pdf"
@@ -88,7 +90,7 @@ set ylabel "{/:Italic d}_{min}, Rugnux (Å)"
 set xrange [%(dlo).2f:%(dhi).2f]; set yrange [%(dlo).2f:%(dhi).2f]
 set xtics (0.5, 1, 2, 4, 8); set ytics (0.5, 1, 2, 4, 8)
 set format x "%%.1f"; set format y "%%.1f"
-set label 12 "%(dn)d\n%(dnf)d\n%(dnb)d" at graph 0.36, graph 0.93 right front
+set label 12 "%(dn)d\n%(dnf)d\n%(dnb)d" at graph 0.31, graph 0.93 right front
 set label 3 "Rugnux deeper: %(deeper)d" at graph 0.95, graph 0.07 right front
 set label 4 "Deposition deeper: %(shallower)d" at graph 0.05, graph 0.68 left front
 plot x ls 1, "%(out)s/dmin.dat" using 1:2 ls 2
@@ -161,6 +163,8 @@ def main():
     ap = argparse.ArgumentParser(description=__doc__.split("\n\n")[0])
     ap.add_argument("runs", nargs="+", help="battery run directories or names (later ones fill in)")
     ap.add_argument("--out", required=True, help="output directory")
+    ap.add_argument("--rfree", choices=["refined", "first-cycle"], default="refined",
+                    help="which REFMAC R-free pair to draw (default: refined, on the shared free set)")
     ap.add_argument("--time-runs", nargs="+", help="runs to draw the time histogram from "
                                                   "(default: the runs above)")
     ap.add_argument("--uncontended", help="a run of the same sets with the GPU to itself, to size the "
@@ -188,11 +192,14 @@ def main():
             excluded.append((s, "both", "verdict fail: " + str(r.get("reason"))))
             continue
         where[s] = source(r["model"])
-        dep, rug = r.get("refmac_rfree_depdata"), r.get("refmac_rfree_depflags")
+        if a.rfree == "refined":
+            dep, rug = r.get("refmac_refined_rfree_shared_depdata"), r.get("refmac_refined_rfree_shared")
+        else:
+            dep, rug = r.get("refmac_rfree_depdata"), r.get("refmac_rfree_depflags")
         if dep and rug:
             rfree.append((dep, rug, s))
         else:
-            excluded.append((s, "rfree", "no REFMAC pair: " + str(r.get("refmac_reason")
+            excluded.append((s, "rfree", "no REFMAC pair: " + str(r.get("refmac_refined_reason") or r.get("refmac_reason")
                                                                    or r.get("dep_reason") or "depositor data not scored")))
         if r.get("d_min_ref") and r.get("d_min"):
             dmin.append((r["d_min_ref"], r["d_min"], s))