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Battery: in-house small-molecule XDS references at full-saturation OVERLOAD

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The XDS references of aspirin (20, 25 keV), citric acid, HEPES and YAG were made with
OVERLOAD=65534, half of the EIGER2's saturation value (133202). CORRECT ignored 13-313
reflections per set whose peak pixel lay between the two - the strongest, most
extinguished reflections - so the references described a data set without them.
Re-ran only the CORRECT step on the unchanged INTEGRATE.HKL with every input parameter
reconstructed from the old CORRECT.LP and OVERLOAD=133201 (saturation - 1, as the other
in-house sets already use); a rerun at 65534 reproduced the old CORRECT.LP. The old outputs
are kept in xds_overload_half/ beside each data set. `refs --write` picked up the new values.

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:
leonarski_f
2026-10-04 06:06:23 +02:00
co-authored by Claude Opus 5.5
parent 122bb4a589
commit c095b19f3a
1 changed files with 5 additions and 5 deletions
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tools/battery/inhouse.json
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@@ -38,11 +38,11 @@
{"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"]},
{"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": 27.97, "completeness": 84.0, "r_meas": 0.032, "cc_half": 0.999, "multiplicity": 3.14, "dmin_low": 2.01, "r_meas_low": 0.03, "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)"},
{"id": "aspirin_x10sa_25keV", "input": "aspirin_x10sa_25keV/aspirin_1_001_master.h5", "wavelength": 0.49594, "cod": "7050897", "tags": ["h5", "monoclinic", "small-molecule"], "ref": {"sgno": 4, "cell": [11.255, 6.541, 11.259, 90.0, 95.916, 90.0], "anomalous": true, "isa": 29.55, "completeness": 86.6, "r_meas": 0.033, "cc_half": 0.999, "multiplicity": 3.15, "dmin_low": 1.63, "r_meas_low": 0.03, "dmin": 0.55, "dmin_rule": "xds_range", "dmin_xds": 0.55, "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)"},
{"id": "citricacid_x10sa_20keV", "input": "citricacid_x10sa_20keV/citricacid_1_005_master.h5", "wavelength": 0.61993, "cod": "5000063", "tags": ["h5", "monoclinic", "small-molecule"], "ref": {"sgno": 4, "cell": [11.454, 5.579, 12.67, 90.0, 111.587, 90.0], "anomalous": true, "isa": 20.55, "completeness": 81.0, "r_meas": 0.04, "cc_half": 0.997, "multiplicity": 3.1, "dmin_low": 2.02, "r_meas_low": 0.043, "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": "anhydrous citric acid, P 21/a (P 21/c in the standard setting); COD 5000063 - J. P. Glusker, J. A. Minkin, A. L. Patterson, Acta Cryst. B25 (1969) 1066-1072, doi:10.1107/S0567740869003542. XDS reports only Sohncke groups (P 21)"},
{"id": "hepes_x10sa_20keV", "input": "hepes_x10sa_20keV/hepes_1_004_master.h5", "wavelength": 0.61993, "cod": "2224210", "tags": ["h5", "orthorhombic", "small-molecule"], "ref": {"sgno": 19, "cell": [8.348, 9.575, 27.068, 90.0, 90.0, 90.0], "anomalous": true, "isa": 28.39, "completeness": 91.6, "r_meas": 0.03, "cc_half": 0.999, "multiplicity": 5.64, "dmin_low": 2.0, "r_meas_low": 0.035, "dmin": 0.68, "dmin_rule": "xds_range", "dmin_xds": 0.68, "dmax": 50.0}, "ref_override": {"sg": "P b c a", "sgno": 61}, "ref_override_why": "HEPES, P b c a; COD 2224210 (100 K, 8.341 9.567 27.066) - P. Sledz, T. Minor, M. Chruszcz, Acta Cryst. E65 (2009) o3027-o3028, doi:10.1107/S1600536809042512. XDS reports only Sohncke groups (P 21 21 21)"},
{"id": "yag_x10sa_20keV", "input": "yag_x10sa_20keV/yag_2_004_master.h5", "wavelength": 0.61993, "cod": "2003066", "tags": ["h5", "cubic", "small-molecule"], "ref": {"sgno": 211, "cell": [11.997, 11.997, 11.997, 90.0, 90.0, 90.0], "anomalous": true, "isa": 3.2, "completeness": 99.0, "r_meas": 0.425, "cc_half": 0.958, "multiplicity": 27.96, "dmin_low": 1.99, "r_meas_low": 0.447, "dmin": 0.68, "dmin_rule": "xds_range", "dmin_xds": 0.68, "dmax": 50.0}, "ref_override": {"sg": "I a -3 d", "sgno": 230}, "ref_override_why": "Y3Al5O12 garnet, I a -3 d; COD 2003066 - A. Nakatsuka, A. Yoshiasa, T. Yamanaka, Acta Cryst. B55 (1999) 266-272, doi:10.1107/S0108768198012567. XDS reports only Sohncke groups (I 4 3 2)"},
{"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)"},
{"id": "aspirin_x10sa_25keV", "input": "aspirin_x10sa_25keV/aspirin_1_001_master.h5", "wavelength": 0.49594, "cod": "7050897", "tags": ["h5", "monoclinic", "small-molecule"], "ref": {"sgno": 4, "cell": [11.255, 6.541, 11.259, 90.0, 95.916, 90.0], "anomalous": true, "isa": 29.25, "completeness": 86.6, "r_meas": 0.034, "cc_half": 0.999, "multiplicity": 3.15, "dmin_low": 1.63, "r_meas_low": 0.032, "dmin": 0.55, "dmin_rule": "xds_range", "dmin_xds": 0.55, "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)"},
{"id": "citricacid_x10sa_20keV", "input": "citricacid_x10sa_20keV/citricacid_1_005_master.h5", "wavelength": 0.61993, "cod": "5000063", "tags": ["h5", "monoclinic", "small-molecule"], "ref": {"sgno": 4, "cell": [11.454, 5.579, 12.67, 90.0, 111.587, 90.0], "anomalous": true, "isa": 20.44, "completeness": 82.0, "r_meas": 0.041, "cc_half": 0.997, "multiplicity": 3.1, "dmin_low": 2.02, "r_meas_low": 0.05, "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": "anhydrous citric acid, P 21/a (P 21/c in the standard setting); COD 5000063 - J. P. Glusker, J. A. Minkin, A. L. Patterson, Acta Cryst. B25 (1969) 1066-1072, doi:10.1107/S0567740869003542. XDS reports only Sohncke groups (P 21)"},
{"id": "hepes_x10sa_20keV", "input": "hepes_x10sa_20keV/hepes_1_004_master.h5", "wavelength": 0.61993, "cod": "2224210", "tags": ["h5", "orthorhombic", "small-molecule"], "ref": {"sgno": 19, "cell": [8.348, 9.575, 27.068, 90.0, 90.0, 90.0], "anomalous": true, "isa": 28.49, "completeness": 91.8, "r_meas": 0.031, "cc_half": 0.999, "multiplicity": 5.66, "dmin_low": 2.0, "r_meas_low": 0.037, "dmin": 0.68, "dmin_rule": "xds_range", "dmin_xds": 0.68, "dmax": 50.0}, "ref_override": {"sg": "P b c a", "sgno": 61}, "ref_override_why": "HEPES, P b c a; COD 2224210 (100 K, 8.341 9.567 27.066) - P. Sledz, T. Minor, M. Chruszcz, Acta Cryst. E65 (2009) o3027-o3028, doi:10.1107/S1600536809042512. XDS reports only Sohncke groups (P 21 21 21)"},
{"id": "yag_x10sa_20keV", "input": "yag_x10sa_20keV/yag_2_004_master.h5", "wavelength": 0.61993, "cod": "2003066", "tags": ["h5", "cubic", "small-molecule"], "ref": {"sgno": 211, "cell": [11.997, 11.997, 11.997, 90.0, 90.0, 90.0], "anomalous": true, "isa": 3.18, "completeness": 99.0, "r_meas": 0.432, "cc_half": 0.947, "multiplicity": 28.44, "dmin_low": 1.99, "r_meas_low": 0.436, "dmin": 0.68, "dmin_rule": "xds_range", "dmin_xds": 0.68, "dmax": 50.0}, "ref_override": {"sg": "I a -3 d", "sgno": 230}, "ref_override_why": "Y3Al5O12 garnet, I a -3 d; COD 2003066 - A. Nakatsuka, A. Yoshiasa, T. Yamanaka, Acta Cryst. B55 (1999) 266-272, doi:10.1107/S0108768198012567. XDS reports only Sohncke groups (I 4 3 2)"},
{"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"}
]}