Battery: in-house standard proteins carry a reference model for R-free and anomalous signal
Each lysozyme, thaumatin, insulin, cytochrome c and myoglobin set names the PDB entry of its crystal form in a `model` field; the runner fetches it like an open-arm deposition and passes it to --model, so the row carries rfree, rmodel_shell_scaled, rfree_deposited/rfree_ratio and the new anom_sigma (ANOMALOUS_SCATTERER_MEAN_SIGMA) - an external yardstick beside the XDS statistics. Reported only: the arm's scoring is unchanged, and the processing is identical with and without the model (19 sets vs all2-full: same space group modulo the model's enantiomorph label, d_min, R_meas, CC1/2, ISa, cell and REFRES table). depdata_check stays open-arm only. Models, chosen by cell/space group and confirmed by rugnux --model: 4AXT lysozyme (6G8A, the coordinates beside the data, has c 2% short: R-free +0.04), 5A47 thaumatin (6G89 +0.06), 2BN3 cubic and 4E7T rhombohedral insulin (bovine; pig 9INS +0.07, human 1MSO +0.08), 4DC8 horse heart myoglobin (b 28.8, not sperm whale's 30.8; 5ZZE equal), 6FF5 bovine cytochrome c - our crystals are a primitive relative of its H32 form (pseudo-centring TNCS), so R-free ~0.49 but the heme iron is the top anomalous peak; 8RKP, the cytochrome c' beside the data, does not fit at all (R-free 0.63, nothing at the iron). Run 20261005-0735_2624a6_inhouse-model (19 sets): R-free 0.18-0.30 on the good sets, 0.37-0.57 on the ISa~2 powder/split myoglobin sweeps and ~0.49 on cytochrome c; anom_sigma rises with wavelength (thaumatin 2.3 at 16 keV, 6.7 at 6.5 keV, 8.9 at 3.8 keV). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
This commit is contained in:
Claude Opus 5.5
+24
-6
@@ -15,7 +15,7 @@ run needed): `cd tools/battery && python3 test_score.py`.
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| arm | datasets | reference | manifest |
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|---|---|---|---|
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| **open** | public PDB depositions of raw diffraction data, plus a few published small-molecule sets | the deposited space group, cell and resolution | `open.json` (committed) |
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| **inhouse** | standard test crystals measured at the SLS (lysozyme, thaumatin, insulin, cytochrome C, myoglobin), small-molecule standards (aspirin, citric acid, HEPES, YAG, L-cystine), plus no-crystal controls | XDS, from the `CORRECT.LP` beside each dataset; for the small molecules the space group is the literature's (`ref_override`), as XDS reports only Sohncke groups; L-cystine, which XDS does not index, has only the literature reference | `inhouse.json` (committed) |
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| **inhouse** | standard test crystals measured at the SLS (lysozyme, thaumatin, insulin, cytochrome C, myoglobin), small-molecule standards (aspirin, citric acid, HEPES, YAG, L-cystine), plus no-crystal controls | XDS, from the `CORRECT.LP` beside each dataset (the standard proteins also carry a reference model for R-free, reported only: `--model` below); for the small molecules the space group is the literature's (`ref_override`), as XDS reports only Sohncke groups; L-cystine, which XDS does not index, has only the literature reference | `inhouse.json` (committed) |
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| **private** | user data | XDS, like inhouse | outside the repository; the local site config gives its path |
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Scoring checks these things in order, and the first one that fails decides the verdict: did it
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@@ -84,7 +84,7 @@ Every set runs **once**, with one command per arm:
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| arm (reference) | command |
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|---|---|
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| open (deposition) | `rugnux -o p --no-export-unmerged --model <deposited coordinates> <input>`; sets without a deposited model (small molecules, unpublished sets, or coordinates that cannot be downloaded) run the same command without `--model` |
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| inhouse, private (XDS) | `rugnux -o p --no-export-unmerged [-A] --report-resolution <XDS d_min>,<XDS d_max> <input>` |
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| inhouse, private (XDS) | `rugnux -o p --no-export-unmerged [-A] --report-resolution <XDS d_min>,<XDS d_max> [--model <reference model>] <input>`; `--model` where the set names one (the in-house standard proteins, below) |
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Neither `--model` nor `--report-resolution` changes the processing: the merged reflections, the
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resolution cut and every decision are the same with and without them (verified bit for bit). So
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@@ -103,6 +103,23 @@ the reference:
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A model that fits may put its enantiomorph on the space-group label; the scorer reads the
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data's own determination instead (`SOHNCKE_SPACE_GROUP` where `SPACE_GROUP_ENANTIOMORPH` is
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`ASSUMED_FROM_MODEL`) and keeps the label in `sg_label`.
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- **`--model`** (in-house standard proteins): a set may name the PDB entry of its crystal form in
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its `model` field; it is fetched and cached like an open-arm entry and passed to `--model`, so
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the row carries the same model fields (`rfree`, `rmodel_shell_scaled`, `rfree_deposited`,
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`rfree_ratio`, `anom_sigma`, ...) - quality on an external yardstick beside the XDS statistics.
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They are reported, never scored: the arm is scored against XDS exactly as without them. One
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entry per crystal form, chosen by cell and space group and confirmed by `rugnux --model` on our
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sets (R-free of the placed model, not refined):
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| sets | model | why |
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|---|---|---|
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| `lyso*` (P4₃2₁2) | 4AXT | hen egg-white lysozyme, 1.1 Å, 100 K, a 78.2 c 37.5 - the middle of our sets' cells (76.9-78.4 / 37.0-37.9); rugnux re-fractionalises the model into the data cell, so the R-free of the placed model rises by a few points per % of cell difference (6G8A, a 78.9 c 36.9: R-free +0.04 on `lyso_x06da_ref`). No ions in the model, so `anom_sigma` is the sulfurs' |
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| `thau*` (P4₁2₁2) | 5A47 | thaumatin from *T. daniellii*, 1.2 Å, a 57.9 c 150.6 (6G89, 2.4 Å: R-free +0.06) |
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| `insu_I*` (I2₁3) | 2BN3 | bovine insulin, cubic, 1.4 Å, 100 K, a 77.9 (9INS, pig, a 78.9, no R-free deposited: R-free +0.07) |
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| `insu_H*` (H3) | 4E7T | bovine T6 2Zn insulin, 1.4 Å, a 81.0 c 33.5 (1MSO, human: R-free +0.08 - our insulin is bovine) |
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| `cytc*` (P3₁21 / P3₂21) | 6FF5 | bovine heart cytochrome c at high ionic strength, H32, a 83.4 c 92.5. Our crystals are a primitive relative of that form - the R centring survives as a pseudo-translation (TNCS, 1/3 2/3 1/3) and c is 4-6% shorter - so the model explains the centred part only and R-free stays near 0.48; the heme iron is still the strongest anomalous peak (17 sigma). Trend only. (8RKP, the cytochrome c' whose P6₂22 cell matches ours, does not fit: R-free 0.63, no density at the iron) |
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| `myob*` (P2₁) | 4DC8 | horse heart myoglobin (b 28.8 Å; sperm whale's P2₁ form has b 30.8), met form with sulfate, 1.5 Å, 100 K, a 35.4 b 28.8 c 63.1 β 106.1 - our setting; the unexposed control of its deposition, so no ligand or modified heme (5ZZE, same form, R-free 0.235 vs 0.233) |
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- **`--report-resolution`** (XDS arms): a second statistics table from the same merge, binned over
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XDS's own range (`dmin_xds` and XDS's d_max as given, 999 included, so it covers exactly what
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XDS's CORRECT.LP totals cover), and `-A` where XDS merged with `FRIEDEL'S_LAW=FALSE` (`"anomalous": true` in the
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@@ -415,9 +432,10 @@ was run `--unforced`), so its forced XDS-arm rows are left out the same way.
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| `isa_ratio`, `r_meas_ratio` | refres_isa / isa_ref and refres_r_meas / r_meas_ref |
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| `cc_half_noise_ratio` | XDS arms: (1/refres_cc_half - 1) / (1/(cc_half_ref - 0.0005) - 1), reported, not scored |
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| `lowres_d`, `lowres_r_meas`, `refres_lowres_d`, `refres_lowres_r_meas`, `lowres_d_ref`, `lowres_r_meas_ref`, `lowres_r_meas_ratio` | the lowest-resolution shell's high-resolution limit and R_meas: rugnux's own table, the reference-range table, XDS's; and refres_lowres_r_meas / lowres_r_meas_ref |
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| `model`, `model_note` | open arm: the deposited coordinates given to `--model`, or why there were none |
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| `rfree`, `rwork`, `cc_model`, `model_fit`, `rfree_deposited`, `rfree_ratio` | open arm with a model: R_FREE, R_WORK, CC_MODEL_OVERALL and MODEL_FIT as rugnux reports them (placement-only, own free set: trend fields), the published R-free, and rfree / rfree_deposited |
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| `rmodel`, `rmodel_shell_scaled`, `radial_misfit` | open arm with a model: R_MODEL, R_MODEL_SHELL_SCALED and MODEL_RADIAL_MISFIT - R over all the reflections, with and without one free scale per resolution shell, and how big that rescale was. `rmodel_shell_scaled` is the R that compares between runs (below) |
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| `model`, `model_note` | open arm, and in-house sets with a `model`: the coordinates given to `--model`, or why there were none |
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| `rfree`, `rwork`, `cc_model`, `model_fit`, `rfree_deposited`, `rfree_ratio` | any row with a model: R_FREE, R_WORK, CC_MODEL_OVERALL and MODEL_FIT as rugnux reports them (placement-only, own free set: trend fields), the published R-free, and rfree / rfree_deposited |
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| `anom_sigma` | any row with a model: ANOMALOUS_SCATTERER_MEAN_SIGMA, the anomalous difference map (F+ - F- on the model's phases) read at every model atom from phosphorus up (S of Met/Cys, metals, Cl, I, ...) and averaged, in map sigma - how much anomalous signal the merge carries; null where the merge kept no Bijvoet split or the model has no such atom |
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| `rmodel`, `rmodel_shell_scaled`, `radial_misfit` | any row with a model: R_MODEL, R_MODEL_SHELL_SCALED and MODEL_RADIAL_MISFIT - R over all the reflections, with and without one free scale per resolution shell, and how big that rescale was. `rmodel_shell_scaled` is the R that compares between runs (below) |
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| `refmac_rfree`, `refmac_rwork`, `refmac_rfree_depflags`, `refmac_rfree_depdata`, `refmac_rfree_ratio`, `refmac_twin`, `refmac_untwinned`, `refmac_status`, `refmac_reason`, `refmac_refined_*`, `refmac_shared_free_n` | the REFMAC check (`--model-check`, open arm; see its section for which R-free is which) |
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| `dep_status`, `dep_reason`, `dep_kind`, `dep_d_min`, `dep_n_common`, `dep_cc_delta_all`, `dep_cc_delta_outer`, `dep_beyond_cc`, `dep_beyond_d` | open arm with a model: our merge against the depositor's data per shell (`depdata_check.py`, above) |
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| `shx_*` | small molecule with a `cod` structure: the SHELXL check (`shelx_check.py`, above) |
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@@ -437,7 +455,7 @@ SVG, no external files):
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the main metrics;
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- plots per set (HTML only; hovering a point shows the set): d_min(rugnux) / d_min(reference)
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for each arm; on the XDS arms the reference-range ISa, R_meas, lowest-shell R_meas and CC1/2
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noise over XDS's; on the open arm R_free / published R_free;
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noise over XDS's; on every row with a model R_free / published R_free;
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- on the open arm, **against the depositor's data**: the per-shell CC difference and the CC past
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the deposited limit, one row per set, sorted by the outer-shell difference;
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- on the XDS arms the **like-for-like table**: the reference-range numbers beside XDS's, with the
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@@ -29,8 +29,9 @@ $JFJOCH_BATTERY_SITE, else site.json beside this script (not committed; site.exa
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Every set runs once, with one command per arm (COMMAND_DOC): the open arm with the deposited model
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(--model), the XDS arms with XDS's range as a report-only second
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table (--report-resolution). Neither option changes the processing, so the one run is both what a
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user gets and the like-for-like comparison.
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table (--report-resolution) and, where a set names the PDB entry of its crystal form, that model
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(--model). Neither option changes the processing, so the one run is both what a user gets and the
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like-for-like comparison.
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A run writes <runs_root>/<YYYYMMDD-HHMM>_<rugnux git>_<label>/ holding a copy of the binary,
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manifest.json (what was run, on what, with which references), results.json (one row per set),
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@@ -73,9 +74,10 @@ PDB_ID = re.compile(r"^[0-9][A-Za-z0-9]{3}$")
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COMMAND_DOC = {
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"deposition": "`rugnux --model <deposited coordinates> <input>` (without --model where there is no "
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"deposited model: small molecules, unpublished sets)",
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"xds": "`rugnux --report-resolution <XDS d_min>,<XDS d_max> <input>`: the second statistics "
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"table at XDS's range is report-only; where XDS kept Friedel mates apart the scorer "
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"reads the run's own per-hand table, which needs no flag",
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"xds": "`rugnux --report-resolution <XDS d_min>,<XDS d_max> [--model <reference model>] <input>`: "
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"the second statistics table at XDS's range is report-only; where XDS kept Friedel mates "
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"apart the scorer reads the run's own per-hand table, which needs no flag. --model where "
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"the set names a PDB entry of its crystal form (the standard proteins)",
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}
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LOCAL_SITE = os.path.join(HERE, "site.json")
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@@ -323,8 +325,9 @@ def failure_note(log):
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def deposited_model(e, opts):
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"""(deposition record from model_check's RCSB cache, None) for the entry a set belongs to, or
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(None, why not). A set id may carry a suffix (6h2p_native); the entry is the part before it."""
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pdb = e["id"].split("_")[0].lower()
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(None, why not). A set id may carry a suffix (6h2p_native); the entry is the part before it.
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An in-house set names the entry of its crystal form in its `model` field instead."""
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pdb = (e.get("model") or e["id"].split("_")[0]).lower()
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if not PDB_ID.match(pdb):
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return None, "no model: not a PDB entry (small molecule or unpublished set)"
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meta = model_check.deposition(pdb, opts["pdb_cache"])
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@@ -344,7 +347,7 @@ def run_one(run_dir, binary, e, opts):
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row.update(score.judge(e, {}, "no input"))
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return row
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meta = None
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if e["reference"] == "deposition":
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if e["reference"] == "deposition" or e.get("model"):
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# no deposited model (small molecule, unpublished): the same command without --model
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meta, row["model_note"] = deposited_model(e, opts)
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if meta:
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@@ -369,7 +372,7 @@ def run_one(run_dir, binary, e, opts):
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row["wall_s"] = row["rugnux_wall_s"] if row["rugnux_wall_s"] is not None else row["elapsed_s"]
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if row["rfree"] and row["rfree_deposited"]:
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row["rfree_ratio"] = round(row["rfree"] / row["rfree_deposited"], 4)
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if row["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
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if e["reference"] == "deposition" and row["model"] and os.path.exists(os.path.join(wd, "p.mtz")):
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row.update(depdata_check.check_set(wd, e["id"], opts["pdb_cache"]))
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if opts["model_check"] and e["arm"] == "open":
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row.update(check_model(e, wd))
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+37
-37
@@ -1,41 +1,41 @@
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{"arm": "inhouse", "aliases": {"E08_lyso_2_006": "lyso_x10sa_90deg_1", "E08_lyso_2_007": "lyso_x10sa_90deg_2", "lyso_2": "lyso_x06da_atten_wedge", "lyso_6_5keV": "lyso_x06da_5keV", "lysoC_14_f46f0a": "lyso_x06da_ice", "Thau_9": "thau_x10sa_0p1deg", "thau_BL1A_1p9A": "thau_bl1a_6p5keV", "thau_BL1A_2p7A": "thau_bl1a_4p6keV", "thau_BL1A_3p3A": "thau_bl1a_3p8keV", "Ins_H_2_fa9841": "insu_H_x06da_twin", "Ins_H_3_d05684": "insu_H_x06da_notwin", "Ins_I_16": "insu_I_x06da_weak", "Ins_I_2_1a530d": "insu_I_x06da_low_isa", "Ins_I_3_5e90e3": "insu_I_x06da_ref", "Ins_I_6_13keV": "insu_I_x06da_13keV", "Ins_I_6_5keV": "insu_I_x06da_5keV", "Ins_I_6_6keV": "insu_I_x06da_6keV", "Ins_I_7_5keV": "insu_I_x06da_5keV_2", "cytC_10": "cytc_x10sa", "cytC_2_0770b5": "cytc_x06da_1", "cytC_3_874285": "cytc_x06da_2", "MyoB_13": "myob_x10sa", "MyoB_9_446b70": "myob_x06da", "MyoB2-1": "myob_x06da_powder_1", "MyoB2-2": "myob_x06da_powder_2", "MyoB2-4": "myob_x06da_split", "MyoB2-5": "myob_x06da_sparse", "onlyice": "nothing_ice", "nothing_3400ac": "nothing_2", "nothing_9bf604": "nothing_1", "lyso_90deg_1": "lyso_x10sa_90deg_1", "lyso_90deg_2": "lyso_x10sa_90deg_2", "lyso_atten_wedge": "lyso_x06da_atten_wedge", "lyso_5keV": "lyso_x06da_5keV", "lyso_ice": "lyso_x06da_ice", "lyso_ref": "lyso_x06da_ref", "lyso_strong": "lyso_x10sa_strong", "lyso_half_image": "lyso_x06da_half_image", "thau_16keV": "thau_x10sa_16keV", "thau_0p1deg": "thau_x10sa_0p1deg", "thau_1p9A": "thau_bl1a_6p5keV", "thau_2p7A": "thau_bl1a_4p6keV", "thau_3p3A": "thau_bl1a_3p8keV", "thau_injection": "thau_x10sa_injection", "thau_pink": "thau_micromax_pink", "insu_H_twin": "insu_H_x06da_twin", "insu_H_notwin": "insu_H_x06da_notwin", "insu_I_weak": "insu_I_x06da_weak", "insu_I_low_isa": "insu_I_x06da_low_isa", "insu_I_ref": "insu_I_x06da_ref", "insu_I_13keV": "insu_I_x06da_13keV", "insu_I_5keV": "insu_I_x06da_5keV", "insu_I_6keV": "insu_I_x06da_6keV", "insu_I_5keV_2": "insu_I_x06da_5keV_2", "cytc_eiger": "cytc_x10sa", "cytc_pilatus_1": "cytc_x06da_1", "cytc_pilatus_2": "cytc_x06da_2", "myob_eiger": "myob_x10sa", "myob_pilatus": "myob_x06da", "myob_powder_1": "myob_x06da_powder_1", "myob_powder_2": "myob_x06da_powder_2", "myob_split": "myob_x06da_split", "myob_aggregate": "myob_x06da_sparse", "myob_x06da_aggregate": "myob_x06da_sparse"}, "sets": [
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{"id": "lyso_x10sa_90deg_1", "input": "lyso_x10sa_90deg_1/lyso_2_006_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [76.879, 76.879, 36.961, 90.0, 90.0, 90.0], "anomalous": true, "isa": 20.75, "completeness": 99.3, "r_meas": 0.182, "cc_half": 0.995, "multiplicity": 3.51, "dmin_low": 5.83, "r_meas_low": 0.049, "dmin": 1.966, "dmin_rule": "xds_range", "dmin_xds": 1.966, "dmax": 50.0}, "tags": ["h5", "lysozyme"]},
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{"id": "lyso_x10sa_90deg_2", "input": "lyso_x10sa_90deg_2/lyso_2_007_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [76.904, 76.904, 36.976, 90.0, 90.0, 90.0], "anomalous": true, "isa": 18.14, "completeness": 99.3, "r_meas": 0.18, "cc_half": 0.994, "multiplicity": 3.51, "dmin_low": 5.86, "r_meas_low": 0.051, "dmin": 1.973, "dmin_rule": "xds_range", "dmin_xds": 1.973, "dmax": 50.0}, "tags": ["h5", "lysozyme"]},
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{"id": "lyso_x06da_atten_wedge", "input": "lyso_x06da_atten_wedge/lyso_2_002_master.h5", "wavelength": 0.95381, "ref": {"sgno": 92, "cell": [78.235, 78.235, 37.798, 90.0, 90.0, 90.0], "anomalous": true, "isa": 16.56, "completeness": 99.9, "r_meas": 0.239, "cc_half": 0.998, "multiplicity": 10.97, "dmin_low": 3.76, "r_meas_low": 0.069, "dmin": 1.264, "dmin_rule": "xds_range", "dmin_xds": 1.264, "dmax": 50.0}, "tags": ["h5", "lysozyme"]},
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{"id": "lyso_x06da_5keV", "input": "lyso_x06da_5keV/lyso_6_001_master.h5", "wavelength": 2.47924, "ref": {"sgno": 92, "cell": [78.225, 78.225, 37.897, 90.0, 90.0, 90.0], "anomalous": true, "isa": 19.36, "completeness": 86.4, "r_meas": 0.064, "cc_half": 0.998, "multiplicity": 8.85, "dmin_low": 7.22, "r_meas_low": 0.047, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "lysozyme", "long-wavelength"]},
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{"id": "lyso_x06da_ice", "input": "lyso_x06da_ice/lysoC_14_56b5b9_master.h5", "wavelength": 0.95364, "ref": {"sgno": 89, "cell": [78.387, 78.387, 37.427, 90.0, 90.0, 90.0], "anomalous": true, "isa": 23.33, "completeness": 100.0, "r_meas": 0.219, "cc_half": 0.998, "multiplicity": 11.86, "dmin_low": 4.26, "r_meas_low": 0.055, "dmin": 1.431, "dmin_rule": "xds_range", "dmin_xds": 1.431, "dmax": 50.0}, "tags": ["h5", "lysozyme"]},
|
||||
{"id": "lyso_x06da_ref", "input": "lyso_x06da_ref/hewl_35_001_master.h5", "wavelength": 0.95329, "ref": {"sgno": 89, "cell": [78.091, 78.091, 37.704, 90.0, 90.0, 90.0], "anomalous": true, "isa": 28.31, "completeness": 100.0, "r_meas": 0.045, "cc_half": 1.0, "multiplicity": 13.76, "dmin_low": 3.58, "r_meas_low": 0.029, "dmin": 1.2, "dmin_rule": "xds_range", "dmin_xds": 1.2, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "tiers": {"smoke": "lysozyme reference set"}},
|
||||
{"id": "lyso_x10sa_strong", "input": "lyso_x10sa_strong/lyso_5_f6ac7e_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [77.769, 77.769, 37.442, 90.0, 90.0, 90.0], "anomalous": false, "isa": 8.63, "completeness": 65.8, "r_meas": 0.112, "cc_half": 0.998, "multiplicity": 11.46, "dmin_low": 3.52, "r_meas_low": 0.077, "dmin": 1.24, "dmin_rule": "cc_half_0.30", "dmin_xds": 1.18, "dmax": 999.0}, "tags": ["h5", "lysozyme"]},
|
||||
{"id": "lyso_x06da_half_image", "input": "lyso_x06da_half_image/lyso3_7_b81d83_master.h5", "wavelength": 0.95373, "ref": {"sgno": 96, "cell": [77.74, 77.74, 37.386, 90.0, 90.0, 90.0], "anomalous": true, "isa": 6.61, "completeness": 99.6, "r_meas": 0.595, "cc_half": 0.958, "multiplicity": 5.31, "dmin_low": 4.91, "r_meas_low": 0.258, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}, "tags": ["h5", "lysozyme"]},
|
||||
{"id": "thau_x10sa_16keV", "input": "thau_x10sa_16keV/lyso_4_d2bb9b_master.h5", "wavelength": 0.77491, "ref": {"sgno": 92, "cell": [57.958, 57.958, 150.547, 90.0, 90.0, 90.0], "anomalous": false, "isa": 44.51, "completeness": 94.3, "r_meas": 0.072, "cc_half": 1.0, "multiplicity": 18.36, "dmin_low": 3.89, "r_meas_low": 0.027, "dmin": 1.3, "dmin_rule": "xds_range", "dmin_xds": 1.3, "dmax": 50.0}, "tags": ["h5", "thaumatin"]},
|
||||
{"id": "thau_x10sa_0p1deg", "input": "thau_x10sa_0p1deg/Thau_9_002_master.h5", "wavelength": 0.99989, "ref": {"sgno": 92, "cell": [58.488, 58.488, 150.788, 90.0, 90.0, 90.0], "anomalous": true, "isa": 9.15, "completeness": 99.0, "r_meas": 0.23, "cc_half": 0.997, "multiplicity": 11.37, "dmin_low": 6.51, "r_meas_low": 0.104, "dmin": 2.197, "dmin_rule": "xds_range", "dmin_xds": 2.197, "dmax": 50.0}, "tags": ["h5", "thaumatin"]},
|
||||
{"id": "thau_bl1a_6p5keV", "input": "thau_bl1a_6p5keV/JTH14_1p9_50ds_90T_k0_JF4M_01_50001_master.h5", "wavelength": 1.9, "ref": {"sgno": 89, "cell": [58.031, 58.031, 150.577, 90.0, 90.0, 90.0], "anomalous": true, "isa": 34.46, "completeness": 91.8, "r_meas": 0.072, "cc_half": 0.999, "multiplicity": 7.95, "dmin_low": 5.33, "r_meas_low": 0.041, "dmin": 1.78, "dmin_rule": "xds_range", "dmin_xds": 1.78, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"]},
|
||||
{"id": "thau_bl1a_4p6keV", "input": "thau_bl1a_4p6keV/JTH14_2p7_50ds_19T_k0_JF4M_01_50001_master.h5", "wavelength": 2.7, "ref": {"sgno": 89, "cell": [58.007, 58.007, 150.511, 90.0, 90.0, 90.0], "anomalous": true, "isa": 35.64, "completeness": 92.0, "r_meas": 0.062, "cc_half": 0.998, "multiplicity": 7.94, "dmin_low": 7.56, "r_meas_low": 0.039, "dmin": 2.53, "dmin_rule": "xds_range", "dmin_xds": 2.53, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"]},
|
||||
{"id": "thau_bl1a_3p8keV", "input": "thau_bl1a_3p8keV/JTH14_3p3_50ds_12T_k0_JF4M_01_50001_master.h5", "wavelength": 3.3, "ref": {"sgno": 89, "cell": [57.895, 57.895, 150.213, 90.0, 90.0, 90.0], "anomalous": true, "isa": 30.8, "completeness": 92.2, "r_meas": 0.057, "cc_half": 0.997, "multiplicity": 7.92, "dmin_low": 9.23, "r_meas_low": 0.039, "dmin": 3.1, "dmin_rule": "xds_range", "dmin_xds": 3.1, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"], "tiers": {"smoke": "long wavelength (3.3 A), KEK BL-1A thaumatin"}},
|
||||
{"id": "thau_x10sa_injection", "input": "thau_x10sa_injection/lyso_13_0c7e7a_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [57.922, 57.922, 150.678, 90.0, 90.0, 90.0], "anomalous": true, "isa": 36.23, "completeness": 86.2, "r_meas": 0.037, "cc_half": 1.0, "multiplicity": 9.96, "dmin_low": 3.83, "r_meas_low": 0.022, "dmin": 1.28, "dmin_rule": "xds_range", "dmin_xds": 1.28, "dmax": 50.0}, "tags": ["h5", "thaumatin"]},
|
||||
{"id": "thau_micromax_pink", "input": "thau_micromax_pink/Thau-Thaumatin_2_master.h5", "wavelength": 0.98419, "ref": {"sgno": 92, "cell": [58.784, 58.784, 152.226, 90.0, 90.0, 90.0], "anomalous": true, "isa": 21.18, "completeness": 98.5, "r_meas": 0.08, "cc_half": 0.999, "multiplicity": 9.38, "dmin_low": 4.17, "r_meas_low": 0.04, "dmin": 1.4, "dmin_rule": "xds_range", "dmin_xds": 1.4, "dmax": 50.0}, "tags": ["h5", "thaumatin", "pink-beam"], "tiers": {"smoke": "pink beam"}},
|
||||
{"id": "lyso_micromax_mono", "input": "lyso_micromax_mono/lysozyme-s6_1_master.h5", "wavelength": 0.95447, "tags": ["h5", "lysozyme"], "ref": {"sgno": 96, "cell": [77.668, 77.668, 37.486, 90.0, 90.0, 90.0], "anomalous": true, "isa": 39.93, "completeness": 100.0, "r_meas": 0.047, "cc_half": 1.0, "multiplicity": 6.22, "dmin_low": 4.54, "r_meas_low": 0.023, "dmin": 1.5, "dmin_rule": "xds_range", "dmin_xds": 1.5, "dmax": 50.0}},
|
||||
{"id": "lyso_micromax_pink", "input": "lyso_micromax_pink/lysozyme-s6_1_master.h5", "wavelength": 0.95374, "tags": ["h5", "lysozyme", "pink-beam"], "ref": {"sgno": 96, "cell": [77.654, 77.654, 37.483, 90.0, 90.0, 90.0], "anomalous": true, "isa": 37.35, "completeness": 99.9, "r_meas": 0.051, "cc_half": 1.0, "multiplicity": 5.96, "dmin_low": 4.39, "r_meas_low": 0.022, "dmin": 1.45, "dmin_rule": "xds_range", "dmin_xds": 1.45, "dmax": 50.0}},
|
||||
{"id": "lysoI_micromax_mono", "input": "lysoI_micromax_mono/lysozyme-Is2_1_master.h5", "wavelength": 0.95447, "tags": ["h5", "lysozyme", "iodine"], "ref": {"sgno": 96, "cell": [78.335, 78.335, 37.46, 90.0, 90.0, 90.0], "anomalous": true, "isa": 31.42, "completeness": 100.0, "r_meas": 0.068, "cc_half": 0.999, "multiplicity": 6.78, "dmin_low": 4.99, "r_meas_low": 0.028, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}},
|
||||
{"id": "lysoI_micromax_pink", "input": "lysoI_micromax_pink/lysozyme-Is2_1_master.h5", "wavelength": 0.95374, "tags": ["h5", "lysozyme", "iodine", "pink-beam"], "ref": {"sgno": 96, "cell": [78.302, 78.302, 37.448, 90.0, 90.0, 90.0], "anomalous": true, "isa": 29.19, "completeness": 100.0, "r_meas": 0.079, "cc_half": 0.999, "multiplicity": 6.8, "dmin_low": 4.99, "r_meas_low": 0.028, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}},
|
||||
{"id": "insu_H_x06da_twin", "input": "insu_H_x06da_twin/Ins_H_2_fa9841_master.h5", "wavelength": 0.95375, "ref": {"sgno": 146, "cell": [81.393, 81.393, 33.272, 90.0, 90.0, 120.0], "anomalous": true, "isa": 6.82, "completeness": 95.0, "r_meas": 0.118, "cc_half": 0.988, "multiplicity": 3.61, "dmin_low": 4.34, "r_meas_low": 0.106, "dmin": 1.455, "dmin_rule": "xds_range", "dmin_xds": 1.455, "dmax": 50.0}, "tags": ["h5", "insulin"]},
|
||||
{"id": "insu_H_x06da_notwin", "input": "insu_H_x06da_notwin/Ins_H_3_d05684_master.h5", "wavelength": 0.95375, "ref": {"sgno": 146, "cell": [81.378, 81.378, 33.269, 90.0, 90.0, 120.0], "anomalous": true, "isa": 17.69, "completeness": 97.4, "r_meas": 0.068, "cc_half": 0.998, "multiplicity": 3.52, "dmin_low": 4.61, "r_meas_low": 0.045, "dmin": 1.544, "dmin_rule": "xds_range", "dmin_xds": 1.544, "dmax": 50.0}, "tags": ["h5", "insulin"], "tiers": {"smoke": "rhombohedral insulin (H3)"}},
|
||||
{"id": "insu_I_x06da_weak", "input": "insu_I_x06da_weak/Ins_16_776a92_master.h5", "wavelength": 0.95373, "ref": {"sgno": 197, "cell": [77.085, 77.085, 77.085, 90.0, 90.0, 90.0], "anomalous": false, "isa": 18.91, "completeness": 92.4, "r_meas": 0.401, "cc_half": 0.999, "multiplicity": 29.04, "dmin_low": 3.22, "r_meas_low": 0.054, "dmin": 1.807, "dmin_rule": "cc_half_0.30", "dmin_xds": 1.08, "dmax": 999.0}, "tags": ["h5", "insulin"]},
|
||||
{"id": "insu_I_x06da_low_isa", "input": "insu_I_x06da_low_isa/Ins_I_2_1a530d_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.582, 77.582, 77.582, 90.0, 90.0, 90.0], "anomalous": true, "isa": 4.15, "completeness": 90.8, "r_meas": 0.22, "cc_half": 0.998, "multiplicity": 13.33, "dmin_low": 3.92, "r_meas_low": 0.167, "dmin": 1.3, "dmin_rule": "xds_range", "dmin_xds": 1.3, "dmax": 50.0}, "tags": ["h5", "insulin"]},
|
||||
{"id": "insu_I_x06da_ref", "input": "insu_I_x06da_ref/Ins_I_3_5e90e3_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.52, 77.52, 77.52, 90.0, 90.0, 90.0], "anomalous": true, "isa": 25.08, "completeness": 100.0, "r_meas": 0.349, "cc_half": 0.998, "multiplicity": 13.82, "dmin_low": 4.82, "r_meas_low": 0.143, "dmin": 1.621, "dmin_rule": "xds_range", "dmin_xds": 1.621, "dmax": 50.0}, "tags": ["h5", "insulin"]},
|
||||
{"id": "insu_I_x06da_13keV", "input": "insu_I_x06da_13keV/Ins_I_6_001_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.468, 77.468, 77.468, 90.0, 90.0, 90.0], "anomalous": true, "isa": 18.83, "completeness": 100.0, "r_meas": 0.279, "cc_half": 0.998, "multiplicity": 17.21, "dmin_low": 4.85, "r_meas_low": 0.093, "dmin": 1.635, "dmin_rule": "xds_range", "dmin_xds": 1.635, "dmax": 50.0}, "tags": ["h5", "insulin"]},
|
||||
{"id": "insu_I_x06da_5keV", "input": "insu_I_x06da_5keV/Ins_I_6_006_master.h5", "wavelength": 2.47923, "ref": {"sgno": 197, "cell": [77.785, 77.785, 77.785, 90.0, 90.0, 90.0], "anomalous": true, "isa": 17.54, "completeness": 91.7, "r_meas": 0.073, "cc_half": 0.999, "multiplicity": 11.17, "dmin_low": 7.21, "r_meas_low": 0.048, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"]},
|
||||
{"id": "insu_I_x06da_6keV", "input": "insu_I_x06da_6keV/Ins_I_6_004_master.h5", "wavelength": 2.06648, "ref": {"sgno": 197, "cell": [77.71, 77.71, 77.71, 90.0, 90.0, 90.0], "anomalous": true, "isa": 17.95, "completeness": 92.4, "r_meas": 0.065, "cc_half": 0.999, "multiplicity": 12.42, "dmin_low": 6.03, "r_meas_low": 0.047, "dmin": 2.04, "dmin_rule": "xds_range", "dmin_xds": 2.04, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"]},
|
||||
{"id": "insu_I_x06da_5keV_2", "input": "insu_I_x06da_5keV_2/Ins_I_7_001_master.h5", "wavelength": 2.47923, "ref": {"sgno": 197, "cell": [77.694, 77.694, 77.694, 90.0, 90.0, 90.0], "anomalous": true, "isa": 20.01, "completeness": 91.8, "r_meas": 0.076, "cc_half": 0.999, "multiplicity": 12.73, "dmin_low": 7.21, "r_meas_low": 0.048, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"], "tiers": {"smoke": "cubic insulin at 5 keV (long wavelength), fast"}},
|
||||
{"id": "cytc_x10sa", "input": "cytc_x10sa/cytC_10_002_master.h5", "wavelength": 0.99989, "ref": {"sgno": 152, "cell": [83.659, 83.659, 86.011, 90.0, 90.0, 120.0], "anomalous": true, "isa": 31.75, "completeness": 99.8, "r_meas": 0.232, "cc_half": 0.999, "multiplicity": 10.65, "dmin_low": 6.05, "r_meas_low": 0.036, "dmin": 2.267, "dmin_rule": "cc_half_0.30", "dmin_xds": 2.039, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"]},
|
||||
{"id": "cytc_x06da_1", "input": "cytc_x06da_1/cytC_2_0770b5_master.h5", "wavelength": 0.95375, "ref": {"sgno": 152, "cell": [83.836, 83.836, 86.733, 90.0, 90.0, 120.0], "anomalous": true, "isa": 24.49, "completeness": 99.9, "r_meas": 0.084, "cc_half": 0.999, "multiplicity": 7.67, "dmin_low": 5.58, "r_meas_low": 0.033, "dmin": 1.875, "dmin_rule": "xds_range", "dmin_xds": 1.875, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"]},
|
||||
{"id": "cytc_x06da_2", "input": "cytc_x06da_2/cytC_3_874285_master.h5", "wavelength": 0.95375, "ref": {"sgno": 152, "cell": [83.719, 83.719, 88.617, 90.0, 90.0, 120.0], "anomalous": true, "isa": 26.98, "completeness": 99.9, "r_meas": 0.097, "cc_half": 0.999, "multiplicity": 7.82, "dmin_low": 5.03, "r_meas_low": 0.032, "dmin": 1.69, "dmin_rule": "xds_range", "dmin_xds": 1.69, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"]},
|
||||
{"id": "myob_x10sa", "input": "myob_x10sa/MyoB_13_110ee0_master.h5", "wavelength": 0.99988, "ref": {"sgno": 4, "cell": [35.229, 28.461, 63.076, 90.0, 106.504, 90.0], "anomalous": true, "isa": 5.21, "completeness": 97.7, "r_meas": 0.247, "cc_half": 0.965, "multiplicity": 3.29, "dmin_low": 5.16, "r_meas_low": 0.186, "dmin": 1.742, "dmin_rule": "xds_range", "dmin_xds": 1.742, "dmax": 50.0}, "tags": ["h5", "myoglobin"]},
|
||||
{"id": "myob_x06da", "input": "myob_x06da/MyoB_9_446b70_master.h5", "wavelength": 0.95365, "ref": {"sgno": 3, "cell": [35.182, 28.544, 62.83, 90.0, 106.138, 90.0], "anomalous": true, "isa": 7.59, "completeness": 99.4, "r_meas": 0.232, "cc_half": 0.987, "multiplicity": 3.47, "dmin_low": 4.23, "r_meas_low": 0.105, "dmin": 1.422, "dmin_rule": "xds_range", "dmin_xds": 1.422, "dmax": 50.0}, "tags": ["h5", "myoglobin"], "tiers": {"smoke": "monoclinic myoglobin, screw not arbitrable by XDS"}, "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)"},
|
||||
{"id": "myob_x06da_powder_1", "input": "myob_x06da_powder_1/MyoB2-1_75979a_master.h5", "wavelength": 0.95373, "ref": {"sgno": 1, "cell": [28.705, 34.796, 64.373, 74.314, 89.879, 90.057], "anomalous": false, "isa": 5.54, "completeness": 74.2, "r_meas": 0.493, "cc_half": 0.966, "multiplicity": 2.87, "dmin_low": 4.44, "r_meas_low": 0.125, "dmin": 1.495, "dmin_rule": "xds_range", "dmin_xds": 1.495, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "tiers": {"smoke": "known hard: triclinic twin"}, "ref_override": {"sg": "P 1 21 1", "sgno": 4, "cell": [35.14, 28.88, 64.64, 90.0, 105.9, 90.0]}, "ref_override_why": "myoglobin, P 1 21 1. XDS indexed this sweep (a powder-contaminated crystal) in P 1 on a reduced cell (28.7 34.8 64.4 74.3 89.9 90.1); the monoclinic cell is that cell's conventional setting"},
|
||||
{"id": "myob_x06da_powder_2", "input": "myob_x06da_powder_2/MyoB2-2_5ddd7d_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.576, 28.811, 63.529, 90.0, 105.593, 90.0], "anomalous": false, "isa": 2.19, "completeness": 58.0, "r_meas": 1.106, "cc_half": 0.655, "multiplicity": 4.71, "dmin_low": 2.98, "r_meas_low": 0.706, "dmin": 0.99, "dmin_rule": "xds_range", "dmin_xds": 0.99, "dmax": 999.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)"},
|
||||
{"id": "myob_x06da_split", "input": "myob_x06da_split/MyoB2-4_079740_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.39, 28.783, 63.626, 90.0, 105.544, 90.0], "anomalous": false, "isa": 12.41, "completeness": 77.7, "r_meas": 0.577, "cc_half": 0.984, "multiplicity": 4.38, "dmin_low": 4.48, "r_meas_low": 0.091, "dmin": 1.506, "dmin_rule": "xds_range", "dmin_xds": 1.506, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)"},
|
||||
{"id": "myob_x06da_sparse", "input": "myob_x06da_sparse/MyoB2-5_7cef9c_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.388, 28.752, 64.083, 90.0, 106.352, 90.0], "anomalous": false, "isa": 5.46, "completeness": 73.7, "r_meas": 0.326, "cc_half": 0.972, "multiplicity": 5.21, "dmin_low": 5.92, "r_meas_low": 0.146, "dmin": 2.0, "dmin_rule": "xds_range", "dmin_xds": 2.0, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)"},
|
||||
{"id": "lyso_x10sa_90deg_1", "input": "lyso_x10sa_90deg_1/lyso_2_006_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [76.879, 76.879, 36.961, 90.0, 90.0, 90.0], "anomalous": true, "isa": 20.75, "completeness": 99.3, "r_meas": 0.182, "cc_half": 0.995, "multiplicity": 3.51, "dmin_low": 5.83, "r_meas_low": 0.049, "dmin": 1.966, "dmin_rule": "xds_range", "dmin_xds": 1.966, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "lyso_x10sa_90deg_2", "input": "lyso_x10sa_90deg_2/lyso_2_007_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [76.904, 76.904, 36.976, 90.0, 90.0, 90.0], "anomalous": true, "isa": 18.14, "completeness": 99.3, "r_meas": 0.18, "cc_half": 0.994, "multiplicity": 3.51, "dmin_low": 5.86, "r_meas_low": 0.051, "dmin": 1.973, "dmin_rule": "xds_range", "dmin_xds": 1.973, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "lyso_x06da_atten_wedge", "input": "lyso_x06da_atten_wedge/lyso_2_002_master.h5", "wavelength": 0.95381, "ref": {"sgno": 92, "cell": [78.235, 78.235, 37.798, 90.0, 90.0, 90.0], "anomalous": true, "isa": 16.56, "completeness": 99.9, "r_meas": 0.239, "cc_half": 0.998, "multiplicity": 10.97, "dmin_low": 3.76, "r_meas_low": 0.069, "dmin": 1.264, "dmin_rule": "xds_range", "dmin_xds": 1.264, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "lyso_x06da_5keV", "input": "lyso_x06da_5keV/lyso_6_001_master.h5", "wavelength": 2.47924, "ref": {"sgno": 92, "cell": [78.225, 78.225, 37.897, 90.0, 90.0, 90.0], "anomalous": true, "isa": 19.36, "completeness": 86.4, "r_meas": 0.064, "cc_half": 0.998, "multiplicity": 8.85, "dmin_low": 7.22, "r_meas_low": 0.047, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "lysozyme", "long-wavelength"], "model": "4axt"},
|
||||
{"id": "lyso_x06da_ice", "input": "lyso_x06da_ice/lysoC_14_56b5b9_master.h5", "wavelength": 0.95364, "ref": {"sgno": 89, "cell": [78.387, 78.387, 37.427, 90.0, 90.0, 90.0], "anomalous": true, "isa": 23.33, "completeness": 100.0, "r_meas": 0.219, "cc_half": 0.998, "multiplicity": 11.86, "dmin_low": 4.26, "r_meas_low": 0.055, "dmin": 1.431, "dmin_rule": "xds_range", "dmin_xds": 1.431, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "lyso_x06da_ref", "input": "lyso_x06da_ref/hewl_35_001_master.h5", "wavelength": 0.95329, "ref": {"sgno": 89, "cell": [78.091, 78.091, 37.704, 90.0, 90.0, 90.0], "anomalous": true, "isa": 28.31, "completeness": 100.0, "r_meas": 0.045, "cc_half": 1.0, "multiplicity": 13.76, "dmin_low": 3.58, "r_meas_low": 0.029, "dmin": 1.2, "dmin_rule": "xds_range", "dmin_xds": 1.2, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "tiers": {"smoke": "lysozyme reference set"}, "model": "4axt"},
|
||||
{"id": "lyso_x10sa_strong", "input": "lyso_x10sa_strong/lyso_5_f6ac7e_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [77.769, 77.769, 37.442, 90.0, 90.0, 90.0], "anomalous": false, "isa": 8.63, "completeness": 65.8, "r_meas": 0.112, "cc_half": 0.998, "multiplicity": 11.46, "dmin_low": 3.52, "r_meas_low": 0.077, "dmin": 1.24, "dmin_rule": "cc_half_0.30", "dmin_xds": 1.18, "dmax": 999.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "lyso_x06da_half_image", "input": "lyso_x06da_half_image/lyso3_7_b81d83_master.h5", "wavelength": 0.95373, "ref": {"sgno": 96, "cell": [77.74, 77.74, 37.386, 90.0, 90.0, 90.0], "anomalous": true, "isa": 6.61, "completeness": 99.6, "r_meas": 0.595, "cc_half": 0.958, "multiplicity": 5.31, "dmin_low": 4.91, "r_meas_low": 0.258, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}, "tags": ["h5", "lysozyme"], "model": "4axt"},
|
||||
{"id": "thau_x10sa_16keV", "input": "thau_x10sa_16keV/lyso_4_d2bb9b_master.h5", "wavelength": 0.77491, "ref": {"sgno": 92, "cell": [57.958, 57.958, 150.547, 90.0, 90.0, 90.0], "anomalous": false, "isa": 44.51, "completeness": 94.3, "r_meas": 0.072, "cc_half": 1.0, "multiplicity": 18.36, "dmin_low": 3.89, "r_meas_low": 0.027, "dmin": 1.3, "dmin_rule": "xds_range", "dmin_xds": 1.3, "dmax": 50.0}, "tags": ["h5", "thaumatin"], "model": "5a47"},
|
||||
{"id": "thau_x10sa_0p1deg", "input": "thau_x10sa_0p1deg/Thau_9_002_master.h5", "wavelength": 0.99989, "ref": {"sgno": 92, "cell": [58.488, 58.488, 150.788, 90.0, 90.0, 90.0], "anomalous": true, "isa": 9.15, "completeness": 99.0, "r_meas": 0.23, "cc_half": 0.997, "multiplicity": 11.37, "dmin_low": 6.51, "r_meas_low": 0.104, "dmin": 2.197, "dmin_rule": "xds_range", "dmin_xds": 2.197, "dmax": 50.0}, "tags": ["h5", "thaumatin"], "model": "5a47"},
|
||||
{"id": "thau_bl1a_6p5keV", "input": "thau_bl1a_6p5keV/JTH14_1p9_50ds_90T_k0_JF4M_01_50001_master.h5", "wavelength": 1.9, "ref": {"sgno": 89, "cell": [58.031, 58.031, 150.577, 90.0, 90.0, 90.0], "anomalous": true, "isa": 34.46, "completeness": 91.8, "r_meas": 0.072, "cc_half": 0.999, "multiplicity": 7.95, "dmin_low": 5.33, "r_meas_low": 0.041, "dmin": 1.78, "dmin_rule": "xds_range", "dmin_xds": 1.78, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"], "model": "5a47"},
|
||||
{"id": "thau_bl1a_4p6keV", "input": "thau_bl1a_4p6keV/JTH14_2p7_50ds_19T_k0_JF4M_01_50001_master.h5", "wavelength": 2.7, "ref": {"sgno": 89, "cell": [58.007, 58.007, 150.511, 90.0, 90.0, 90.0], "anomalous": true, "isa": 35.64, "completeness": 92.0, "r_meas": 0.062, "cc_half": 0.998, "multiplicity": 7.94, "dmin_low": 7.56, "r_meas_low": 0.039, "dmin": 2.53, "dmin_rule": "xds_range", "dmin_xds": 2.53, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"], "model": "5a47"},
|
||||
{"id": "thau_bl1a_3p8keV", "input": "thau_bl1a_3p8keV/JTH14_3p3_50ds_12T_k0_JF4M_01_50001_master.h5", "wavelength": 3.3, "ref": {"sgno": 89, "cell": [57.895, 57.895, 150.213, 90.0, 90.0, 90.0], "anomalous": true, "isa": 30.8, "completeness": 92.2, "r_meas": 0.057, "cc_half": 0.997, "multiplicity": 7.92, "dmin_low": 9.23, "r_meas_low": 0.039, "dmin": 3.1, "dmin_rule": "xds_range", "dmin_xds": 3.1, "dmax": 100.0}, "tags": ["h5", "thaumatin", "long-wavelength"], "tiers": {"smoke": "long wavelength (3.3 A), KEK BL-1A thaumatin"}, "model": "5a47"},
|
||||
{"id": "thau_x10sa_injection", "input": "thau_x10sa_injection/lyso_13_0c7e7a_master.h5", "wavelength": 0.99988, "ref": {"sgno": 92, "cell": [57.922, 57.922, 150.678, 90.0, 90.0, 90.0], "anomalous": true, "isa": 36.23, "completeness": 86.2, "r_meas": 0.037, "cc_half": 1.0, "multiplicity": 9.96, "dmin_low": 3.83, "r_meas_low": 0.022, "dmin": 1.28, "dmin_rule": "xds_range", "dmin_xds": 1.28, "dmax": 50.0}, "tags": ["h5", "thaumatin"], "model": "5a47"},
|
||||
{"id": "thau_micromax_pink", "input": "thau_micromax_pink/Thau-Thaumatin_2_master.h5", "wavelength": 0.98419, "ref": {"sgno": 92, "cell": [58.784, 58.784, 152.226, 90.0, 90.0, 90.0], "anomalous": true, "isa": 21.18, "completeness": 98.5, "r_meas": 0.08, "cc_half": 0.999, "multiplicity": 9.38, "dmin_low": 4.17, "r_meas_low": 0.04, "dmin": 1.4, "dmin_rule": "xds_range", "dmin_xds": 1.4, "dmax": 50.0}, "tags": ["h5", "thaumatin", "pink-beam"], "tiers": {"smoke": "pink beam"}, "model": "5a47"},
|
||||
{"id": "lyso_micromax_mono", "input": "lyso_micromax_mono/lysozyme-s6_1_master.h5", "wavelength": 0.95447, "tags": ["h5", "lysozyme"], "ref": {"sgno": 96, "cell": [77.668, 77.668, 37.486, 90.0, 90.0, 90.0], "anomalous": true, "isa": 39.93, "completeness": 100.0, "r_meas": 0.047, "cc_half": 1.0, "multiplicity": 6.22, "dmin_low": 4.54, "r_meas_low": 0.023, "dmin": 1.5, "dmin_rule": "xds_range", "dmin_xds": 1.5, "dmax": 50.0}, "model": "4axt"},
|
||||
{"id": "lyso_micromax_pink", "input": "lyso_micromax_pink/lysozyme-s6_1_master.h5", "wavelength": 0.95374, "tags": ["h5", "lysozyme", "pink-beam"], "ref": {"sgno": 96, "cell": [77.654, 77.654, 37.483, 90.0, 90.0, 90.0], "anomalous": true, "isa": 37.35, "completeness": 99.9, "r_meas": 0.051, "cc_half": 1.0, "multiplicity": 5.96, "dmin_low": 4.39, "r_meas_low": 0.022, "dmin": 1.45, "dmin_rule": "xds_range", "dmin_xds": 1.45, "dmax": 50.0}, "model": "4axt"},
|
||||
{"id": "lysoI_micromax_mono", "input": "lysoI_micromax_mono/lysozyme-Is2_1_master.h5", "wavelength": 0.95447, "tags": ["h5", "lysozyme", "iodine"], "ref": {"sgno": 96, "cell": [78.335, 78.335, 37.46, 90.0, 90.0, 90.0], "anomalous": true, "isa": 31.42, "completeness": 100.0, "r_meas": 0.068, "cc_half": 0.999, "multiplicity": 6.78, "dmin_low": 4.99, "r_meas_low": 0.028, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}, "model": "4axt"},
|
||||
{"id": "lysoI_micromax_pink", "input": "lysoI_micromax_pink/lysozyme-Is2_1_master.h5", "wavelength": 0.95374, "tags": ["h5", "lysozyme", "iodine", "pink-beam"], "ref": {"sgno": 96, "cell": [78.302, 78.302, 37.448, 90.0, 90.0, 90.0], "anomalous": true, "isa": 29.19, "completeness": 100.0, "r_meas": 0.079, "cc_half": 0.999, "multiplicity": 6.8, "dmin_low": 4.99, "r_meas_low": 0.028, "dmin": 1.65, "dmin_rule": "xds_range", "dmin_xds": 1.65, "dmax": 50.0}, "model": "4axt"},
|
||||
{"id": "insu_H_x06da_twin", "input": "insu_H_x06da_twin/Ins_H_2_fa9841_master.h5", "wavelength": 0.95375, "ref": {"sgno": 146, "cell": [81.393, 81.393, 33.272, 90.0, 90.0, 120.0], "anomalous": true, "isa": 6.82, "completeness": 95.0, "r_meas": 0.118, "cc_half": 0.988, "multiplicity": 3.61, "dmin_low": 4.34, "r_meas_low": 0.106, "dmin": 1.455, "dmin_rule": "xds_range", "dmin_xds": 1.455, "dmax": 50.0}, "tags": ["h5", "insulin"], "model": "4e7t"},
|
||||
{"id": "insu_H_x06da_notwin", "input": "insu_H_x06da_notwin/Ins_H_3_d05684_master.h5", "wavelength": 0.95375, "ref": {"sgno": 146, "cell": [81.378, 81.378, 33.269, 90.0, 90.0, 120.0], "anomalous": true, "isa": 17.69, "completeness": 97.4, "r_meas": 0.068, "cc_half": 0.998, "multiplicity": 3.52, "dmin_low": 4.61, "r_meas_low": 0.045, "dmin": 1.544, "dmin_rule": "xds_range", "dmin_xds": 1.544, "dmax": 50.0}, "tags": ["h5", "insulin"], "tiers": {"smoke": "rhombohedral insulin (H3)"}, "model": "4e7t"},
|
||||
{"id": "insu_I_x06da_weak", "input": "insu_I_x06da_weak/Ins_16_776a92_master.h5", "wavelength": 0.95373, "ref": {"sgno": 197, "cell": [77.085, 77.085, 77.085, 90.0, 90.0, 90.0], "anomalous": false, "isa": 18.91, "completeness": 92.4, "r_meas": 0.401, "cc_half": 0.999, "multiplicity": 29.04, "dmin_low": 3.22, "r_meas_low": 0.054, "dmin": 1.807, "dmin_rule": "cc_half_0.30", "dmin_xds": 1.08, "dmax": 999.0}, "tags": ["h5", "insulin"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_low_isa", "input": "insu_I_x06da_low_isa/Ins_I_2_1a530d_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.582, 77.582, 77.582, 90.0, 90.0, 90.0], "anomalous": true, "isa": 4.15, "completeness": 90.8, "r_meas": 0.22, "cc_half": 0.998, "multiplicity": 13.33, "dmin_low": 3.92, "r_meas_low": 0.167, "dmin": 1.3, "dmin_rule": "xds_range", "dmin_xds": 1.3, "dmax": 50.0}, "tags": ["h5", "insulin"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_ref", "input": "insu_I_x06da_ref/Ins_I_3_5e90e3_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.52, 77.52, 77.52, 90.0, 90.0, 90.0], "anomalous": true, "isa": 25.08, "completeness": 100.0, "r_meas": 0.349, "cc_half": 0.998, "multiplicity": 13.82, "dmin_low": 4.82, "r_meas_low": 0.143, "dmin": 1.621, "dmin_rule": "xds_range", "dmin_xds": 1.621, "dmax": 50.0}, "tags": ["h5", "insulin"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_13keV", "input": "insu_I_x06da_13keV/Ins_I_6_001_master.h5", "wavelength": 0.95375, "ref": {"sgno": 197, "cell": [77.468, 77.468, 77.468, 90.0, 90.0, 90.0], "anomalous": true, "isa": 18.83, "completeness": 100.0, "r_meas": 0.279, "cc_half": 0.998, "multiplicity": 17.21, "dmin_low": 4.85, "r_meas_low": 0.093, "dmin": 1.635, "dmin_rule": "xds_range", "dmin_xds": 1.635, "dmax": 50.0}, "tags": ["h5", "insulin"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_5keV", "input": "insu_I_x06da_5keV/Ins_I_6_006_master.h5", "wavelength": 2.47923, "ref": {"sgno": 197, "cell": [77.785, 77.785, 77.785, 90.0, 90.0, 90.0], "anomalous": true, "isa": 17.54, "completeness": 91.7, "r_meas": 0.073, "cc_half": 0.999, "multiplicity": 11.17, "dmin_low": 7.21, "r_meas_low": 0.048, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_6keV", "input": "insu_I_x06da_6keV/Ins_I_6_004_master.h5", "wavelength": 2.06648, "ref": {"sgno": 197, "cell": [77.71, 77.71, 77.71, 90.0, 90.0, 90.0], "anomalous": true, "isa": 17.95, "completeness": 92.4, "r_meas": 0.065, "cc_half": 0.999, "multiplicity": 12.42, "dmin_low": 6.03, "r_meas_low": 0.047, "dmin": 2.04, "dmin_rule": "xds_range", "dmin_xds": 2.04, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"], "model": "2bn3"},
|
||||
{"id": "insu_I_x06da_5keV_2", "input": "insu_I_x06da_5keV_2/Ins_I_7_001_master.h5", "wavelength": 2.47923, "ref": {"sgno": 197, "cell": [77.694, 77.694, 77.694, 90.0, 90.0, 90.0], "anomalous": true, "isa": 20.01, "completeness": 91.8, "r_meas": 0.076, "cc_half": 0.999, "multiplicity": 12.73, "dmin_low": 7.21, "r_meas_low": 0.048, "dmin": 2.45, "dmin_rule": "xds_range", "dmin_xds": 2.45, "dmax": 50.0}, "tags": ["h5", "insulin", "long-wavelength"], "tiers": {"smoke": "cubic insulin at 5 keV (long wavelength), fast"}, "model": "2bn3"},
|
||||
{"id": "cytc_x10sa", "input": "cytc_x10sa/cytC_10_002_master.h5", "wavelength": 0.99989, "ref": {"sgno": 152, "cell": [83.659, 83.659, 86.011, 90.0, 90.0, 120.0], "anomalous": true, "isa": 31.75, "completeness": 99.8, "r_meas": 0.232, "cc_half": 0.999, "multiplicity": 10.65, "dmin_low": 6.05, "r_meas_low": 0.036, "dmin": 2.267, "dmin_rule": "cc_half_0.30", "dmin_xds": 2.039, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"], "model": "6ff5"},
|
||||
{"id": "cytc_x06da_1", "input": "cytc_x06da_1/cytC_2_0770b5_master.h5", "wavelength": 0.95375, "ref": {"sgno": 152, "cell": [83.836, 83.836, 86.733, 90.0, 90.0, 120.0], "anomalous": true, "isa": 24.49, "completeness": 99.9, "r_meas": 0.084, "cc_half": 0.999, "multiplicity": 7.67, "dmin_low": 5.58, "r_meas_low": 0.033, "dmin": 1.875, "dmin_rule": "xds_range", "dmin_xds": 1.875, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"], "model": "6ff5"},
|
||||
{"id": "cytc_x06da_2", "input": "cytc_x06da_2/cytC_3_874285_master.h5", "wavelength": 0.95375, "ref": {"sgno": 152, "cell": [83.719, 83.719, 88.617, 90.0, 90.0, 120.0], "anomalous": true, "isa": 26.98, "completeness": 99.9, "r_meas": 0.097, "cc_half": 0.999, "multiplicity": 7.82, "dmin_low": 5.03, "r_meas_low": 0.032, "dmin": 1.69, "dmin_rule": "xds_range", "dmin_xds": 1.69, "dmax": 50.0}, "tags": ["h5", "cytochrome-c"], "model": "6ff5"},
|
||||
{"id": "myob_x10sa", "input": "myob_x10sa/MyoB_13_110ee0_master.h5", "wavelength": 0.99988, "ref": {"sgno": 4, "cell": [35.229, 28.461, 63.076, 90.0, 106.504, 90.0], "anomalous": true, "isa": 5.21, "completeness": 97.7, "r_meas": 0.247, "cc_half": 0.965, "multiplicity": 3.29, "dmin_low": 5.16, "r_meas_low": 0.186, "dmin": 1.742, "dmin_rule": "xds_range", "dmin_xds": 1.742, "dmax": 50.0}, "tags": ["h5", "myoglobin"], "model": "4dc8"},
|
||||
{"id": "myob_x06da", "input": "myob_x06da/MyoB_9_446b70_master.h5", "wavelength": 0.95365, "ref": {"sgno": 3, "cell": [35.182, 28.544, 62.83, 90.0, 106.138, 90.0], "anomalous": true, "isa": 7.59, "completeness": 99.4, "r_meas": 0.232, "cc_half": 0.987, "multiplicity": 3.47, "dmin_low": 4.23, "r_meas_low": 0.105, "dmin": 1.422, "dmin_rule": "xds_range", "dmin_xds": 1.422, "dmax": 50.0}, "tags": ["h5", "myoglobin"], "tiers": {"smoke": "monoclinic myoglobin, screw not arbitrable by XDS"}, "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)", "model": "4dc8"},
|
||||
{"id": "myob_x06da_powder_1", "input": "myob_x06da_powder_1/MyoB2-1_75979a_master.h5", "wavelength": 0.95373, "ref": {"sgno": 1, "cell": [28.705, 34.796, 64.373, 74.314, 89.879, 90.057], "anomalous": false, "isa": 5.54, "completeness": 74.2, "r_meas": 0.493, "cc_half": 0.966, "multiplicity": 2.87, "dmin_low": 4.44, "r_meas_low": 0.125, "dmin": 1.495, "dmin_rule": "xds_range", "dmin_xds": 1.495, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "tiers": {"smoke": "known hard: triclinic twin"}, "ref_override": {"sg": "P 1 21 1", "sgno": 4, "cell": [35.14, 28.88, 64.64, 90.0, 105.9, 90.0]}, "ref_override_why": "myoglobin, P 1 21 1. XDS indexed this sweep (a powder-contaminated crystal) in P 1 on a reduced cell (28.7 34.8 64.4 74.3 89.9 90.1); the monoclinic cell is that cell's conventional setting", "model": "4dc8"},
|
||||
{"id": "myob_x06da_powder_2", "input": "myob_x06da_powder_2/MyoB2-2_5ddd7d_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.576, 28.811, 63.529, 90.0, 105.593, 90.0], "anomalous": false, "isa": 2.19, "completeness": 58.0, "r_meas": 1.106, "cc_half": 0.655, "multiplicity": 4.71, "dmin_low": 2.98, "r_meas_low": 0.706, "dmin": 0.99, "dmin_rule": "xds_range", "dmin_xds": 0.99, "dmax": 999.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)", "model": "4dc8"},
|
||||
{"id": "myob_x06da_split", "input": "myob_x06da_split/MyoB2-4_079740_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.39, 28.783, 63.626, 90.0, 105.544, 90.0], "anomalous": false, "isa": 12.41, "completeness": 77.7, "r_meas": 0.577, "cc_half": 0.984, "multiplicity": 4.38, "dmin_low": 4.48, "r_meas_low": 0.091, "dmin": 1.506, "dmin_rule": "xds_range", "dmin_xds": 1.506, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)", "model": "4dc8"},
|
||||
{"id": "myob_x06da_sparse", "input": "myob_x06da_sparse/MyoB2-5_7cef9c_master.h5", "wavelength": 0.95373, "ref": {"sgno": 3, "cell": [35.388, 28.752, 64.083, 90.0, 106.352, 90.0], "anomalous": false, "isa": 5.46, "completeness": 73.7, "r_meas": 0.326, "cc_half": 0.972, "multiplicity": 5.21, "dmin_low": 5.92, "r_meas_low": 0.146, "dmin": 2.0, "dmin_rule": "xds_range", "dmin_xds": 2.0, "dmax": 50.0}, "tags": ["h5", "myoglobin", "twin"], "ref_override": {"sg": "P 1 21 1", "sgno": 4}, "ref_override_why": "myoglobin, P 1 21 1. XDS does not judge screw axes (it reports P 2)", "model": "4dc8"},
|
||||
{"id": "nothing_2", "input": "nothing_2/test-28_3400ac_master.h5", "wavelength": 0.99988, "expect": "no_lattice", "tags": ["h5", "control"]},
|
||||
{"id": "nothing_1", "input": "nothing_1/test-28_9bf604_master.h5", "wavelength": 0.99988, "expect": "no_lattice", "tags": ["h5", "control"]},
|
||||
{"id": "aspirin_x10sa_20keV", "input": "aspirin_x10sa_20keV/aspirin_1_002_master.h5", "wavelength": 0.61993, "cod": "7050897", "tags": ["h5", "monoclinic", "small-molecule"], "ref": {"sgno": 4, "cell": [11.262, 6.543, 11.257, 90.0, 95.916, 90.0], "anomalous": true, "isa": 27.4, "completeness": 84.0, "r_meas": 0.033, "cc_half": 0.999, "multiplicity": 3.14, "dmin_low": 2.01, "r_meas_low": 0.033, "dmin": 0.68, "dmin_rule": "xds_range", "dmin_xds": 0.68, "dmax": 50.0}, "ref_override": {"sg": "P 1 21/c 1", "sgno": 14}, "ref_override_why": "aspirin form I, P 21/c; COD 7050897 - C. C. Wilson, New J. Chem. 26 (2002) 1733-1739, doi:10.1039/b203775k. XDS reports only Sohncke groups (P 21)"},
|
||||
|
||||
+12
-3
@@ -23,6 +23,7 @@ NOISE = {
|
||||
"rfree": ("abs", 0.005),
|
||||
"rmodel_shell_scaled": ("abs", 0.005),
|
||||
"radial_misfit": ("abs", 0.05),
|
||||
"anom_sigma": ("rel", 0.05),
|
||||
"refres_r_meas": ("rel", 0.05),
|
||||
"refres_isa": ("rel", 0.05),
|
||||
"refres_lowres_r_meas": ("rel", 0.05),
|
||||
@@ -249,7 +250,7 @@ def changes(ra, rb):
|
||||
out.append(name)
|
||||
# The R that is comparable between runs, and the radial profile that decides whether `rfree`
|
||||
# beside it can be read at all (both only where both runs carry them).
|
||||
for name in ("rmodel_shell_scaled", "radial_misfit", "rfree"):
|
||||
for name in ("rmodel_shell_scaled", "radial_misfit", "rfree", "anom_sigma"):
|
||||
if ra.get(name) is not None and rb.get(name) is not None and beyond_noise(name, ra[name], rb[name]):
|
||||
out.append(name)
|
||||
# the like-for-like table only where both runs have one (a pre-schema-3 run has none)
|
||||
@@ -282,7 +283,7 @@ def arrow(x, y, fmt=lambda v: str(v)):
|
||||
|
||||
def compare_table(doc, rows, only_changed=True):
|
||||
head = ["set", "arm", "verdict", "space group", "d_min", "ISa", "R_meas", "CC1/2",
|
||||
"cell dev %", "R_model (shell-scaled)", "R_free", "radial misfit",
|
||||
"cell dev %", "R_model (shell-scaled)", "R_free", "radial misfit", "anom. sigma",
|
||||
"ref-range R_meas", "ref-range low-res R_meas", "SHELXL R1", "SHELXL wR2", "SHELXL GooF",
|
||||
"SHELXL EXTI", "time s", "beyond noise"]
|
||||
out = []
|
||||
@@ -300,6 +301,7 @@ def compare_table(doc, rows, only_changed=True):
|
||||
arrow(ra.get("rmodel_shell_scaled"), rb.get("rmodel_shell_scaled"), lambda v: f"{v:.3f}"),
|
||||
arrow(ra.get("rfree"), rb.get("rfree"), lambda v: f"{v:.3f}"),
|
||||
arrow(ra.get("radial_misfit"), rb.get("radial_misfit"), lambda v: f"{v:.2f}"),
|
||||
arrow(ra.get("anom_sigma"), rb.get("anom_sigma"), lambda v: f"{v:.2f}"),
|
||||
arrow(ra.get("refres_r_meas"), rb.get("refres_r_meas"), lambda v: f"{100 * v:.1f}%"),
|
||||
arrow(ra.get("refres_lowres_r_meas"), rb.get("refres_lowres_r_meas"),
|
||||
lambda v: f"{100 * v:.1f}%"),
|
||||
@@ -439,6 +441,7 @@ def build(run_dir, baseline=None, allow_incomplete=False):
|
||||
("rfree", "R_free (placement, within-run only)", "{:.3f}"),
|
||||
("radial_misfit", "radial misfit", "{:.2f}"),
|
||||
("rfree_ratio", "R_free ratio", "{:.3f}"),
|
||||
("anom_sigma", "anomalous map at the scatterers, sigma", "{:.2f}"),
|
||||
("refmac_rfree_ratio", "REFMAC R_free ratio", "{:.3f}"),
|
||||
("dep_cc_delta_all", "dCC vs depositor, all", "{:+.3f}"),
|
||||
("dep_cc_delta_outer", "dCC vs depositor, outer 2 shells", "{:+.3f}"),
|
||||
@@ -618,10 +621,16 @@ def build(run_dir, baseline=None, allow_incomplete=False):
|
||||
"read in a delta table. Radial misfit is how big that per-shell rescale had to be (the "
|
||||
"RMS of its logarithm): when it moves between two runs, R_free between them means "
|
||||
"little. Both are reported for a human to judge; nothing is scored on them.")
|
||||
if any(r.get("anom_sigma") for r in res):
|
||||
doc.p("Anom. sigma is the anomalous difference map (F+ - F- on the model's phases) read at the "
|
||||
"model's anomalous scatterers - every atom from phosphorus up: the S of Met and Cys, "
|
||||
"metals, Cl, I - and averaged, in units of the map's r.m.s.: how much anomalous signal "
|
||||
"the merge carries, on the model's yardstick. Reported, never scored.")
|
||||
model = [("R_model (shell-scaled)", "rmodel_shell_scaled"), ("radial misfit", "radial_misfit"),
|
||||
("CC model", "cc_model"), ("R_free (within-run)", "rfree"), ("R_work", "rwork"),
|
||||
("dep R_free", "rfree_deposited"),
|
||||
("R_free ratio", "rfree_ratio")] if any(r.get("rfree") for r in res) else []
|
||||
("R_free ratio", "rfree_ratio"),
|
||||
("anom. sigma", "anom_sigma")] if any(r.get("rfree") for r in res) else []
|
||||
model += [("REFMAC R_free", "refmac_rfree_depflags"), ("REFMAC dep data", "refmac_rfree_depdata"),
|
||||
("REFMAC ratio", "refmac_rfree_ratio")] if any(r.get("refmac_status") for r in res) else []
|
||||
model += [("dCC dep. outer", "dep_cc_delta_outer")] if any(r.get("dep_status") for r in res) else []
|
||||
|
||||
@@ -197,9 +197,13 @@ def judge(entry, rep, run_note):
|
||||
"r_meas_ref": ref.get("r_meas"), "cc_half_ref": ref.get("cc_half"), "isa_ref": ref.get("isa"),
|
||||
"completeness_ref": ref.get("completeness"), "multiplicity_ref": ref.get("multiplicity"),
|
||||
"sg_relation": None,
|
||||
# rugnux's own fit of the deposited model (--model, open arm): a rigid-body placement scored
|
||||
# on rugnux's own free set, so a trend number, not the depositor's R-free
|
||||
# rugnux's own fit of the deposited model (--model; the open arm, and the in-house sets that
|
||||
# name a model): a rigid-body placement scored on rugnux's own free set, so a trend number,
|
||||
# not the depositor's R-free
|
||||
"rfree": fnum(rep.get("R_FREE")), "rwork": fnum(rep.get("R_WORK")),
|
||||
# the anomalous difference map's mean height (sigma) at the model's anomalous scatterers
|
||||
# (P and heavier: S, metals, Cl, I, ...) - how much anomalous signal the merge carries
|
||||
"anom_sigma": fnum(rep.get("ANOMALOUS_SCATTERER_MEAN_SIGMA")),
|
||||
"model_fit": rep.get("MODEL_FIT"), "cc_model": fnum(rep.get("CC_MODEL_OVERALL")),
|
||||
# R over ALL the reflections, with and without one free scale per resolution shell, and the
|
||||
# size of that rescale. rfree above describes one run and is not comparable with another's:
|
||||
|
||||
Reference in New Issue
Block a user