diff --git a/tools/battery/README.md b/tools/battery/README.md index 6de6fb989..8011a1832 100644 --- a/tools/battery/README.md +++ b/tools/battery/README.md @@ -23,7 +23,7 @@ data): `cd tools/battery && python3 doc_check.py`. | arm | datasets | reference | manifest | |---|---|---|---| | **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) | -| **inhouse** | standard test crystals measured at the SLS (lysozyme, thaumatin, insulin, cytochrome C, myoglobin), small-molecule standards (aspirin, citric acid, HEPES, YAG, KDP, L-cystine, L-ascorbic acid, NaCl), 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) | +| **inhouse** | standard test crystals measured at the SLS (lysozyme, thaumatin, insulin, cytochrome C, myoglobin), small-molecule standards (aspirin, citric acid, HEPES, YAG, KDP, L-cystine, L-ascorbic acid, NaCl, L-glutamic acid), 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) | | **private** | user data | XDS, like inhouse | outside the repository; the local site config gives its path | | **refine** | public PDB depositions whose structure factors and coordinates go through refinement only, nothing processed | none: a set passes when the refinement ran; the R-factors and the solvent audit are reported | `refine.json` (committed) | | **multisweep** | several sweeps merged as one - small wedges of several crystals, several sweeps of one crystal (swung detector, kappa runs, repeated sweeps), small molecules - plus must-not-merge controls; opt-in, never part of a default run | the base row's: each row names an open or in-house row (`base`), whose reference scores the merge as that arm scores it, plus which sweeps joined (`sweeps_expect`, below) | `multisweep.json` (committed) | diff --git a/tools/battery/doc_check.py b/tools/battery/doc_check.py index dcc8989c8..d07ce54f8 100644 --- a/tools/battery/doc_check.py +++ b/tools/battery/doc_check.py @@ -31,7 +31,8 @@ INHOUSE = {"lyso": "lysozyme", "lysoI": "lysozyme", "thau": "thaumatin", "insu": "cytc": "cytochrome C", "myob": "myoglobin", "nothing": "no-crystal controls", "aspirin": "aspirin", "citricacid": "citric acid", "hepes": "HEPES", "yag": "YAG", "kdp": "KDP", "lcystine": "L-cystine", "lascorbate": "L-ascorbic acid", - "nacl": "NaCl"} + "nacl": "NaCl", + "lglutamate": "L-glutamic acid"} errors = [] diff --git a/tools/battery/inhouse.json b/tools/battery/inhouse.json index 279c67493..e299c8ac8 100644 --- a/tools/battery/inhouse.json +++ b/tools/battery/inhouse.json @@ -48,5 +48,6 @@ {"id": "nacl_x10sa_20keV", "input": "salt_x10sa/SaltPL_002_master.h5", "wavelength": 0.61993, "cod": "2108652", "tags": ["h5", "cubic", "small-molecule"], "ref": {"sgno": 209, "cell": [5.608, 5.608, 5.608, 90.0, 90.0, 90.0], "anomalous": false, "isa": 2.49, "completeness": 100.0, "r_meas": 0.379, "cc_half": 0.97, "multiplicity": 27.5, "dmin_low": 1.93, "r_meas_low": 0.339, "cc_half_high": 0.995, "dmin": 0.78, "dmin_rule": "xds_range", "dmin_xds": 0.78, "dmax": 50.0}, "ref_override": {"sg": "F m -3 m", "sgno": 225}, "ref_override_why": "rock salt (halite, NaCl), F m -3 m; COD 2108652 (a 5.6035, R 0.015) - V. Tsirelson, A. Stash, Acta Cryst. B76 (2020) 769-778, doi:10.1107/S2052520620009178. XDS reports only Sohncke groups (F 4 3 2); XDS indexed only its 150 strongest spots, given that group and the cell (several grains 5-10 deg apart; README_XDS beside the data)", "tiers": {"smoke": "known hard: tiny cubic F cell (rock salt), several grains, 99% of spots on powder rings; rc184 named the lattice tI and merged in I422"}}, {"id": "lascorbate", "input": "lascorbate/lascorbate_1_a39733_master.h5", "wavelength": 0.49594, "tags": ["h5", "orthorhombic", "small-molecule"], "ref": {"sgno": 19, "cell": [4.439, 8.496, 18.921, 90.0, 90.0, 90.0], "anomalous": false, "isa": 17.97, "completeness": 39.6, "r_meas": 0.039, "cc_half": 0.999, "multiplicity": 8.82, "dmin_low": 1.66, "r_meas_low": 0.037, "cc_half_high": 0.996, "dmin": 0.56, "dmin_rule": "xds_range", "dmin_xds": 0.56, "dmax": 50.0}}, {"id": "lcystine_x10sa_20keV", "input": "lcystine_x10sa_20keV/lcystine_2_004_master.h5", "wavelength": 0.61993, "cod": "1513328", "tags": ["h5", "hexagonal", "small-molecule"], "ref_override": {"sg": "P 61 2 2", "sgno": 178, "cell": [5.422, 5.422, 56.275, 90.0, 90.0, 120.0]}, "ref_override_why": "hexagonal L-cystine, P 61 2 2; COD 5000005 - B. M. Oughton and P. M. Harrison, Acta Cryst. 12 (1959) 396-404, doi:10.1107/S0365110X59001177. No XDS reference: XDS indexes under 10% of the spots of either sweep, so the row is scored on lattice and symmetry only"}, - {"id": "lcystine_x10sa_25keV", "input": "lcystine_x10sa_25keV/lcystine_2_003_master.h5", "wavelength": 0.49594, "cod": "1513328", "tags": ["h5", "hexagonal", "small-molecule"], "ref_override": {"sg": "P 61 2 2", "sgno": 178, "cell": [5.422, 5.422, 56.275, 90.0, 90.0, 120.0]}, "ref_override_why": "hexagonal L-cystine, P 61 2 2; COD 5000005 - B. M. Oughton and P. M. Harrison, Acta Cryst. 12 (1959) 396-404, doi:10.1107/S0365110X59001177. No XDS reference: XDS indexes under 10% of the spots of either sweep, so the row is scored on lattice and symmetry only"} + {"id": "lcystine_x10sa_25keV", "input": "lcystine_x10sa_25keV/lcystine_2_003_master.h5", "wavelength": 0.49594, "cod": "1513328", "tags": ["h5", "hexagonal", "small-molecule"], "ref_override": {"sg": "P 61 2 2", "sgno": 178, "cell": [5.422, 5.422, 56.275, 90.0, 90.0, 120.0]}, "ref_override_why": "hexagonal L-cystine, P 61 2 2; COD 5000005 - B. M. Oughton and P. M. Harrison, Acta Cryst. 12 (1959) 396-404, doi:10.1107/S0365110X59001177. No XDS reference: XDS indexes under 10% of the spots of either sweep, so the row is scored on lattice and symmetry only"}, + {"id": "lglutamate_x10sa_20keV", "input": "lglutamate/lglutamate_3_002_master.h5", "wavelength": 0.619927, "tags": ["h5", "orthorhombic", "small-molecule"], "ref": {"sgno": 19, "cell": [5.13, 6.882, 17.253, 90.0, 90.0, 90.0], "anomalous": false, "isa": 10.52, "completeness": 50.0, "r_meas": 0.073, "cc_half": 0.998, "multiplicity": 10.25, "dmin_low": 2.05, "r_meas_low": 0.059, "cc_half_high": 0.98, "dmin": 0.7, "dmin_rule": "xds_range", "dmin_xds": 0.7, "dmax": 50.0}} ]}