searchindex.js

Search.setIndex({"alltitles": {"Acknowledgements": [[0, null]], "Background": [[1, null]], "Changes since 0.2.2.2": [[13, "changes-since-0-2-2-2"]], "Changes since 0.2.2.3": [[13, "changes-since-0-2-2-3"]], "Changes since 0.2.2.4": [[13, "changes-since-0-2-2-4"]], "Changes since 0.2.3": [[13, "changes-since-0-2-3"]], "Changes since 0.2.4": [[13, "changes-since-0-2-4"]], "Changes since 0.2.5": [[13, "changes-since-0-2-5"]], "Changes since 0.2.5.1 - big changes in bold": [[13, "changes-since-0-2-5-1-big-changes-in-bold"]], "Changes since 0.2.5.2": [[13, "changes-since-0-2-5-2"]], "Changes since 0.2.6.0": [[13, "changes-since-0-2-6-0"]], "Changes since 0.2.6.1": [[13, "changes-since-0-2-6-1"]], "Changes since 0.2.6.2": [[13, "changes-since-0-2-6-2"]], "Changes since 0.2.6.3": [[13, "changes-since-0-2-6-3"]], "Changes since 0.2.6.4": [[13, "changes-since-0-2-6-4"]], "Changes since 0.2.6.5": [[13, "changes-since-0-2-6-5"]], "Changes since 0.2.6.6": [[13, "changes-since-0-2-6-6"]], "Changes since 0.2.7.0": [[13, "changes-since-0-2-7-0"]], "Changes since 0.2.7.2": [[13, "changes-since-0-2-7-2"]], "Changes since 0.3.0.0": [[13, "changes-since-0-3-0-0"]], "Changes since 0.3.0.3": [[13, "changes-since-0-3-0-3"]], "Changes since 0.3.0.4": [[13, "changes-since-0-3-0-4"]], "Changes since 0.3.0.5": [[13, "changes-since-0-3-0-5"]], "Changes since 0.3.0.6": [[13, "changes-since-0-3-0-6"]], "Changes since 0.3.1.0": [[13, "changes-since-0-3-1-0"]], "Changes since 0.3.1.6": [[13, "changes-since-0-3-1-6"]], "Changes since 0.3.1.7": [[13, "changes-since-0-3-1-7"]], "Changes since 0.3.2.0": [[13, "changes-since-0-3-2-0"]], "Changes since 0.3.3.0": [[13, "changes-since-0-3-3-0"]], "Changes since 0.3.3.1": [[13, "changes-since-0-3-3-1"]], "Changes since 0.3.3.2": [[13, "changes-since-0-3-3-2"]], "Changes since 0.3.3.3": [[13, "changes-since-0-3-3-3"]], "Changes since 0.3.3.4": [[13, "changes-since-0-3-3-4"]], "Changes since 0.3.4.0": [[13, "changes-since-0-3-4-0"]], "Changes since 0.3.5.0": [[13, "changes-since-0-3-5-0"]], "Changes since 0.3.5.1: CCP4 patch release": [[13, "changes-since-0-3-5-1-ccp4-patch-release"]], "Changes since 0.3.5.2: dealing with huge data sets": [[13, "changes-since-0-3-5-2-dealing-with-huge-data-sets"]], "Changes since 0.3.6.1: New XDS etc.": [[13, "changes-since-0-3-6-1-new-xds-etc"]], "Changes since 0.3.6.2: Cope with new CCP4.": [[13, "changes-since-0-3-6-2-cope-with-new-ccp4"]], "Changes since 0.3.6.3: Bug fixes, add CC-half, removing Scala.": [[13, "changes-since-0-3-6-3-bug-fixes-add-cc-half-removing-scala"]], "Changes since 0.3.7.0: Added DIALS (mostly)": [[13, "changes-since-0-3-7-0-added-dials-mostly"]], "Changes since 0.3.8.0": [[13, "changes-since-0-3-8-0"]], "Comments": [[2, null]], "Commonly used program options": [[10, "commonly-used-program-options"]], "Contact": [[3, "contact"]], "Data Integration": [[14, "data-integration"]], "Data Reduction": [[14, "data-reduction"]], "Dose series - the dose_series_repeat option": [[16, "dose-series-the-dose-series-repeat-option"]], "Dose series - using a grouping.yml file": [[16, "dose-series-using-a-grouping-yml-file"]], "Generalised merge grouping on metadata": [[16, "generalised-merge-grouping-on-metadata"]], "HTML pages": [[11, "html-pages"]], "Installation": [[4, null]], "Insulin tutorial": [[5, null]], "Introduction": [[3, null], [6, null]], "Introductory example": [[7, null]], "Merging SSX data in groups with xia2": [[16, null]], "Merging in groups": [[14, "merging-in-groups"]], "Modifying input": [[7, "modifying-input"]], "Overcoming difficulties in geometry refinement": [[14, "overcoming-difficulties-in-geometry-refinement"]], "Overcoming problems with the detector geometry for SSX data": [[17, null]], "Parallel data processing": [[9, "parallel-data-processing"]], "Parameters": [[10, null]], "Phil parameters": [[10, "phil-parameters"]], "Processing multi-crystal datasets with xia2": [[9, null]], "Processing serial synchrotron crystallography (SSX) datasets with xia2": [[14, null]], "Program output": [[11, null]], "Quick start guide": [[12, null]], "Refining multi-panel detectors": [[17, "refining-multi-panel-detectors"]], "Relaxing restraints in refinement": [[17, "relaxing-restraints-in-refinement"]], "Release notes": [[13, null]], "Resolution limits": [[10, "resolution-limits"]], "Setting the detector distance/beam centre": [[17, "setting-the-detector-distance-beam-centre"]], "Using xia2": [[15, null]], "xia2 license": [[8, null]], "xia2.txt": [[11, "xia2-txt"]]}, "docnames": ["acknowledgements", "background", "comments", "index", "installation", "insulin_tutorial", "introduction", "introductory_example", "license", "multi_crystal", "parameters", "program_output", "quick_start", "release_notes", "serial_crystallography", "using_xia2", "xia2-ssx-dose-series", "xia2-ssx-geometry-refinement"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["acknowledgements.rst", "background.rst", "comments.rst", "index.rst", "installation.rst", "insulin_tutorial.rst", "introduction.rst", "introductory_example.rst", "license.rst", "multi_crystal.rst", "parameters.rst", "program_output.rst", "quick_start.rst", "release_notes.rst", "serial_crystallography.rst", "using_xia2.rst", "xia2-ssx-dose-series.rst", "xia2-ssx-geometry-refinement.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [4, 13], "0": [5, 7, 9, 10, 11, 14, 15, 16, 17], "00": 11, "000": [7, 13], "0001": 17, "011": 7, "0123": 17, "014": 7, "020": 7, "022": 7, "023": 7, "034": 7, "036": 7, "036539": 17, "03654": 17, "036547": 17, "036579": 17, "036764": 17, "03769": 17, "038": 7, "039968": 17, "041": 7, "04204": 17, "042045": 17, "042079": 17, "042274": 17, "043": 7, "043169": 17, "043361": 17, "045247": 17, "04756": 17, "048249": 17, "051901": 17, "05244": 17, "056994": 17, "057296": 17, "0579": 17, "060": 7, "062588": 17, "063433": 17, "063907": 17, "070151": 17, "070669": 17, "080024": 17, "085": 7, "088303": 17, "09": 13, "091092": 17, "0951": 17, "095794": 17, "096": 7, "1": [0, 1, 4, 5, 7, 9, 10, 11, 14, 15, 16, 17], "10": [7, 9, 10, 13, 17], "100": [10, 13], "1000": 14, "10005": 17, "1001": 17, "10247": 17, "1025": 17, "10335": 17, "105": 7, "10815": 17, "11": 17, "11034": 17, "113": 7, "115": 17, "11538": 17, "118": 7, "118588": 7, "12": [7, 13, 17], "120": 13, "1200": 17, "121": 7, "12287": 13, "1245": 17, "125": 1, "126": 0, "12819": 17, "129": 7, "13": [13, 17], "13055": 17, "131": 7, "132": 1, "136": 0, "14": 5, "140": 11, "149": 11, "15": 13, "150": 17, "1513": 13, "15792": 17, "15923": 17, "16": 9, "1634": 7, "165": 13, "17": 13, "18": 7, "180": 13, "18595": 17, "186": 2, "189": 11, "19": 7, "190": 2, "199": 7, "1994": 1, "2": [0, 1, 5, 7, 9, 10, 14, 16, 17], "20": 7, "200": [7, 13], "2000": 17, "2002": 0, "2005": 1, "2006": [0, 1, 8], "2008": 13, "2009": 8, "200mb": 13, "2010": [1, 2], "2011": [7, 15], "2018": 0, "20879": 17, "21677": 17, "21902": 17, "21934": 17, "21954": 17, "22": 7, "24": 7, "24372": 17, "25": [7, 10, 13, 17], "250": [13, 14, 17], "26076": 17, "267": 7, "27": 7, "270": 13, "272": 7, "2829": 17, "290": 11, "297": 7, "2d": 13, "2dold": 13, "2dr": 13, "2m": 11, "2x2": 13, "3": [0, 1, 7, 10, 14, 17], "30": [5, 13], "300k": 13, "317": 17, "337": 7, "339": 7, "34": 7, "342": 7, "345": 17, "349": 13, "35": [0, 13], "355": 7, "368": 7, "37": 7, "38": [14, 17], "3802": 17, "3d": [2, 4, 5, 7, 10, 12, 13, 15], "3dd": 10, "3di": [4, 10, 13], "3dii": [2, 4, 5, 10, 12, 13, 15], "3dold": 13, "3dr": 13, "4": [1, 5, 7, 9, 10, 17], "41": 7, "43": 2, "448": 7, "45": [7, 11, 13], "450": [7, 9, 11, 15], "46": 11, "48": 1, "49": 7, "491": 7, "5": [5, 7, 10, 15, 16, 17], "50": [5, 11, 13], "5027": 17, "50875": 7, "51": 11, "52": [7, 11], "529": 7, "53": 11, "544": 7, "55": 7, "553": 7, "5595": 17, "564": 7, "5680": 17, "57": [1, 11], "57757": 17, "58": 7, "59": 11, "5969": 17, "5a": 13, "6": [0, 7, 17], "60": [7, 11, 13], "608": 13, "61": 11, "6194": 17, "62": 7, "63": 7, "633": 7, "6331": 17, "6382": 17, "65": 17, "679": 7, "68147": 17, "6m": 13, "7": [7, 17], "70": [7, 17], "72": [0, 1], "74765": 17, "760": 1, "763": 1, "77": 7, "779": 7, "78986": 17, "79": [14, 17], "791": 7, "79187": 17, "8": [5, 7, 9, 14, 17], "80": 17, "81": 11, "82": [0, 1, 13], "82114": 17, "85": [0, 7], "86": 7, "89": [11, 13], "9": [7, 17], "90": [5, 11, 13, 14, 17], "93": [7, 11], "931": 7, "95": [7, 11], "95258": 17, "95269": 17, "9552": 7, "97": 0, "9749": 7, "979000": 5, "979500": [9, 15], "99": [11, 13], "9999": 17, "A": [1, 2, 5, 8, 9, 14, 15, 17], "AND": 8, "AS": 8, "As": [7, 10, 11, 15, 16, 17], "At": [1, 7], "BE": 8, "BUT": 8, "BY": 8, "By": [4, 9, 11, 16, 17], "FOR": 8, "For": [2, 13, 14, 15, 16, 17], "IF": 8, "IN": 8, "If": [4, 5, 9, 10, 11, 12, 13, 14, 17], "In": [0, 1, 3, 4, 6, 9, 14, 16, 17], "It": [3, 6, 7, 13, 14, 16, 17], "NO": 8, "NOT": [8, 13], "No": [13, 17], "OF": 8, "ON": 8, "OR": 8, "On": 9, "SUCH": 8, "THE": 8, "TO": 8, "The": [0, 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 17], "Then": 14, "There": [5, 10, 11, 17], "These": [7, 13, 15], "To": [4, 13, 14, 16, 17], "WILL": 13, "Will": 13, "a1": 14, "a2": 14, "aa_sequ": 5, "abandon": [11, 13], "abil": 10, "abl": [9, 13, 14], "about": [1, 13, 17], "abov": [8, 10, 16, 17], "absenc": 14, "ac": 4, "access": [3, 6, 13], "accord": 13, "accordingli": 16, "accur": [13, 17], "accuraci": [14, 17], "achiev": 7, "acknowledg": 8, "acta": [0, 1], "action": 17, "actual": 13, "add": [4, 5, 17], "addit": [0, 13], "addition": [0, 5, 9, 14], "address": 17, "adjust": [7, 13, 14, 15], "adsc": 13, "advis": 8, "aforement": 1, "after": [4, 7, 13, 14, 17], "again": 5, "against": [1, 13], "aggreg": 14, "aid": 13, "aimless": [4, 5, 10, 11, 12, 13, 15], "al": [0, 13], "algorithm": 17, "all": [3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "allow": [3, 6, 9, 11, 13, 14, 17], "almost": 13, "along": [11, 13, 17], "alpha": 13, "alphabet": 5, "alreadi": 14, "also": [2, 4, 5, 8, 11, 13, 14, 16, 17], "altern": [9, 13, 17], "although": 16, "altogeth": 9, "alwai": [2, 4, 13], "ambigu": 14, "amount": 13, "amplitud": 1, "an": [3, 4, 5, 6, 7, 9, 10, 13, 14, 15, 16, 17], "analys": 13, "analysi": [0, 1, 2, 7, 13, 14], "andrew": [0, 13], "ani": [4, 8, 9, 13], "annoi": 13, "anomal": [5, 7, 10, 12, 13, 14, 15], "anoth": 17, "answer": [2, 13], "anyon": [1, 3, 6], "anyth": 2, "ap": 11, "appear": [9, 12, 13], "appl": 0, "appli": [2, 5, 13], "applic": 13, "approach": 17, "appropri": [5, 11, 13], "approxim": 7, "ar": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17], "area": 13, "argument": 13, "aris": 8, "around": 13, "arrai": 16, "arriv": 17, "ask": 2, "assess": [5, 13], "assign": [7, 13, 15, 17], "assist": [0, 3, 6, 13], "assum": 5, "assumpt": [5, 14], "asu": 5, "atom": [5, 7, 10, 12, 13, 15], "author": [0, 1], "auto": [10, 17], "auto_reduct": 17, "autoindex": [5, 11, 13], "autom": [1, 10, 13, 16, 17], "automat": [1, 5, 9, 10, 13, 14, 15], "avail": [1, 4, 5, 9, 13, 14, 16, 17], "averag": 13, "avoid": 13, "ax": 17, "axi": 17, "b": [7, 10, 13], "b_sol": 14, "ba": [7, 15], "back": 13, "background": 13, "bad": [11, 13, 17], "bar": 5, "barium": 7, "base": [10, 13, 16], "basi": [10, 13], "basic": 15, "batch": [7, 11, 13, 14, 17], "batch_": [14, 16], "batch_siz": 14, "bbsrc": [0, 1], "beam": [5, 9, 13, 14], "beamlin": [1, 3, 6, 10, 13], "becaus": 2, "becom": [1, 17], "been": [0, 11, 13, 14, 17], "befor": [9, 13, 15, 16], "begin": [5, 9, 15], "begun": 13, "behalf": [3, 6, 11], "behaviour": [10, 11, 16], "being": [1, 13], "below": [5, 7, 11, 14, 15, 16, 17], "benchmark": [3, 6], "best": [2, 13], "beta": 13, "better": 13, "between": [13, 17], "bib": 13, "bibtex": 13, "bigger": 13, "bin": [7, 13], "binari": [8, 13], "bind": 13, "binsort_scr": 13, "bioxhit": [0, 13], "blank": [11, 13], "block": [13, 16], "blog": [3, 4], "blogspot": 3, "both": [2, 9, 13], "bragg": 13, "brighter": 1, "broadest": 15, "broken": 13, "bsd": [0, 8, 13], "build": 13, "built": [1, 14], "bulk": 14, "bundl": [4, 13], "busi": [3, 6, 8], "bz2": 5, "c": [8, 10, 13], "c2": [5, 13], "cach": 13, "cad": 13, "calcul": 13, "calibr": 17, "call": 13, "can": [4, 5, 9, 10, 13, 14, 16, 17], "capabl": [0, 13], "capac": 13, "card": 13, "care": 13, "carefulli": 13, "case": [3, 5, 6, 11, 13, 14, 16, 17], "caus": [8, 13], "cbf": [9, 13, 14, 16], "cbflib": 13, "cc_half": [10, 13], "cc_half_method": 10, "ccd": 17, "cclrc": 8, "ccp4": [0, 1, 4, 8, 15], "cctbx": [0, 13], "ce": 14, "ce2": 14, "ce3": 14, "cell": [9, 10, 11, 13, 14], "center": 0, "centr": [5, 9, 13, 14], "centroid": 17, "centrosymmetr": 10, "certain": 10, "certainli": [2, 13], "chale": 13, "chang": [5, 10, 14, 17], "channel": 13, "charact": [5, 11], "characteris": 13, "check": [4, 5, 13], "check_xds_vers": 13, "chef": 13, "chip1": 14, "chip2": 14, "chiral": 10, "choic": 13, "chooch": 13, "chunk": 13, "cif": 14, "citat": [11, 13], "cite": 2, "class": 13, "classif": 16, "clean": 13, "cleaner": 13, "cleanli": 13, "clear": 7, "clearli": [0, 7], "close": [13, 17], "clue": 13, "cluster": [9, 13, 14], "clutter": 13, "co": 3, "code": [3, 8, 13], "collect": [5, 13], "colspot": 10, "column": 13, "com": [3, 4, 11, 13], "combin": 5, "come": [5, 13], "command": [4, 5, 7, 9, 10, 13, 14, 15, 16, 17], "commandlin": 13, "comment": 5, "common": [1, 9, 14, 17], "commonli": 1, "compar": 17, "complain": 13, "complet": [7, 13], "complex": [5, 7, 13, 14], "complic": 16, "comprehens": [10, 13], "comput": [2, 13], "conclus": [9, 13], "condit": [8, 17], "configur": [0, 13], "conjunct": 9, "consequenti": 8, "consist": [7, 11, 14], "constant": [10, 13, 16], "constitut": 17, "contain": [13, 14, 15, 16, 17], "content": [5, 14], "continu": 9, "contract": 8, "contribut": 13, "contributor": 8, "control": [13, 14, 16], "conveni": 11, "convent": [5, 13], "converg": [13, 17], "coordin": 17, "coorind": 17, "cope": 5, "copi": [5, 13], "copyright": 8, "core": [1, 13], "corner": [13, 17], "correct": [5, 10, 13, 17], "correctli": [0, 2, 3, 5, 6, 9, 13, 16], "correl": 7, "correspond": [14, 15], "corrupt": 13, "cosym": 14, "could": 13, "count": 17, "counts_fractional_loss": 10, "coupl": 9, "cours": [0, 12], "cover": [15, 16], "cowan": [5, 13], "crash": 13, "creat": [13, 14, 16, 17], "criteria": 13, "criterion": 13, "critic": [4, 11, 12], "crucial": 1, "cruft": 13, "cryst": [0, 1], "crystal": [5, 10, 11, 13, 14, 15, 16, 17], "crystallograph": 13, "crystallographi": [1, 2, 13, 16, 17], "csh": 13, "cspad": 17, "ctruncat": 13, "cubic": 5, "cumbersom": 17, "cumul": 7, "current": [4, 9, 13], "custom": [16, 17], "customis": [13, 14], "cut": 13, "cutoff": [14, 16], "cycl": [13, 17], "d": [1, 13], "d50": 1, "d62": [0, 1], "d66": 1, "d74": 0, "d_max": 10, "d_min": [5, 7, 10, 14, 16], "daili": 10, "damag": [7, 8, 13], "data": [0, 1, 2, 3, 5, 6, 7, 8, 10, 11, 15], "data1": 5, "data_reduct": [14, 16], "datafil": [11, 13, 14], "dataset": [7, 15, 16, 17], "dataset_1": 9, "dataset_2": 9, "date": 13, "david": 13, "de": 4, "dead": 17, "debug": [11, 13], "dec": 13, "decid": 13, "decis": [1, 7, 13], "decreas": 17, "dectri": 17, "default": [9, 10, 13, 14, 15, 16, 17], "defin": 16, "definit": [13, 16], "defpix": 10, "deg": 17, "degre": 13, "deleg": 13, "demo": 5, "demonst": 16, "demonstr": [5, 7], "denot": 10, "depend": [2, 4, 8, 17], "deposit": 13, "depositfil": 13, "deprec": [10, 13], "deriv": [8, 13], "describ": [1, 3, 5, 6, 14, 17], "descript": [9, 14, 15], "design": [11, 13, 17], "detail": [0, 10, 14, 15], "detect": [13, 17], "detect_blank": 10, "detector": [1, 13, 14], "determin": [13, 14], "develop": [0, 1], "dial": [0, 2, 4, 5, 9, 10, 12, 14, 15, 16, 17], "dials_env": 4, "dials_import": 17, "diamond": [0, 7, 8, 13], "dice": 13, "diederich": [0, 13], "diffdump": 13, "differ": [7, 13, 14, 17], "diffract": [0, 1, 3, 6, 7, 13, 17], "diffractionimag": 13, "direct": [8, 17], "directli": 13, "directori": [4, 5, 9, 11, 13, 14, 15, 16], "disabl": 9, "disclaim": 8, "discov": 17, "discuss": [0, 7, 11], "disk": [2, 13], "displai": [11, 13, 17], "distanc": [5, 13, 14], "distribut": [0, 4, 8, 13], "divid": 13, "divis": 13, "dl": [7, 13, 15], "dna": 7, "do": [5, 7, 12, 13, 17], "document": [8, 10, 11, 12, 14], "doe": [13, 16, 17], "doesn": [5, 12], "don": [9, 10, 12, 13], "done": 13, "dose": [11, 13, 14, 15], "dose_1": 16, "dose_2": 16, "dose_3": 16, "dose_4": 16, "dose_5": 16, "dose_point": 16, "dose_series_repeat": 14, "download": 4, "downstream": 1, "dry": 12, "due": [14, 17], "duplic": 13, "dure": [0, 13], "durin": 10, "dxtbx": 13, "e": [0, 1, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17], "each": [5, 9, 11, 13, 14, 16, 17], "easi": 7, "easier": [9, 13], "echo": 13, "edit": 17, "editor": [5, 17], "effect": 13, "effici": [9, 16], "effort": 2, "eh2": 13, "ehtpx_xml_out": 13, "eiger": 10, "either": 13, "elimin": 13, "els": [2, 13], "elsewher": 13, "email": 4, "emax": 10, "enabl": [13, 14, 17], "encount": 9, "end": [0, 3, 4, 5, 6, 7, 9, 10, 15, 17], "endors": 8, "engin": 17, "enough": [14, 17], "ensur": [1, 9, 13], "entiti": 17, "entri": 16, "environ": 13, "epoch": 5, "equal": 9, "equip": [3, 6, 13], "equival": [13, 16], "error": [9, 13, 17], "essenti": 7, "estim": [10, 13, 14], "estimate_resolut": 10, "et": 0, "eu": 0, "evalu": [13, 14], "evan": [0, 1], "even": [8, 13], "event": [8, 11], "everi": [13, 16], "everyon": 8, "everyth": [11, 13], "exactli": 9, "exampl": [3, 5, 6, 9, 13, 14, 15, 16, 17], "example1": 17, "example2": 17, "except": 13, "exception": 13, "exclud": 13, "execut": 13, "exemplari": 8, "exist": [13, 17], "expect": [10, 13, 14], "experi": [5, 9, 14, 15, 16, 17], "experiment": [7, 13, 17], "expert": [3, 6, 14], "expertis": 1, "explain": 5, "explicit": 13, "explicitli": [5, 13, 14], "express": [8, 13], "expt": [14, 16, 17], "extend": 13, "extens": 17, "extent": 13, "extra": 13, "extract": 14, "extrem": 13, "f": [5, 13], "face": 17, "facil": [1, 3, 6, 16], "fact": 17, "factor": [1, 7, 13], "fail": [9, 13, 17], "failov": [9, 13], "failur": [11, 17], "fair": 13, "fake": 13, "fall": 13, "fals": [9, 10, 14], "far": 17, "fast": [5, 17], "fast_axi": 17, "fast_mod": 5, "fast_slow_beam_centr": 17, "faster": [1, 9], "favourit": 5, "featur": [9, 16], "feedback": 14, "feel": 2, "fertil": 1, "few": [14, 16], "fewer": 13, "fft1d": 10, "fft3d": 10, "ficat": 0, "fiddl": 4, "figur": 7, "file": [5, 9, 10, 11, 13, 14, 15, 17], "filepath": 16, "filter": [14, 17], "filter_ice_r": 10, "final": [8, 9, 13, 14], "find": [4, 13], "find_spot": [10, 14], "fine": 13, "finish": 13, "first": [7, 9, 13, 14, 15, 17], "fit": 8, "fix": 17, "fix_list": 17, "flag": [13, 17], "focu": [3, 6], "folder": [14, 16], "follow": [4, 5, 7, 8, 11, 13, 14, 15, 16, 17], "foo": [5, 13], "forkinitegr": 13, "forkintegr": [4, 13], "form": [5, 8, 13, 16, 17], "formal": 16, "formalis": 16, "format": [11, 13, 14, 16, 17], "former": 13, "formula": 16, "forth": 13, "forthcom": 13, "found": [5, 10, 12, 13, 15], "four": 13, "fraction": [13, 14], "frame": [7, 13, 17], "framework": [0, 17], "francoi": 13, "free": 13, "freer": 13, "freer_fil": 13, "freer_flag": 13, "from": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "full": [7, 13, 14], "fulli": 17, "function": [7, 13], "further": [10, 14, 17], "furthermor": 9, "furthest": 13, "futur": 13, "fvnqhlcgshlvealylvcgergffytpka": 5, "g": [1, 2, 7, 9, 10, 11, 13, 14, 16, 17], "g4": 13, "g5": 13, "gain": 13, "gamma": 13, "gap": 13, "gaussnewton": 17, "gave": 13, "gener": [10, 11, 13, 14, 15, 16], "generalis": 14, "genom": 0, "geometri": 13, "geometry_refin": [14, 17], "get": [1, 2, 5, 12, 13, 15], "gildea": 13, "github": [3, 4, 13], "give": [3, 6, 7, 11, 13, 14, 17], "given": [9, 13, 14, 17], "giveqccasvcslyqlenycn": 5, "glanc": 11, "global": 13, "gmail": [3, 4, 11], "goe": 13, "good": [2, 8, 11, 13, 14, 17], "gracefulli": 13, "graem": [5, 8], "graphic": 11, "great": 13, "greater": 13, "gremlin": 13, "grid": 13, "gross": 0, "ground": 1, "group": [9, 13, 17], "group_1": 16, "group_2": 16, "group_3": 16, "group_4": 16, "group_5": 16, "guess": [5, 13], "gui": 15, "guid": 15, "guidanc": 17, "gunk": 13, "gw56": 13, "gxparm": 13, "gz": 5, "h": 13, "h5": [14, 16, 17], "ha": [0, 2, 3, 5, 6, 11, 13, 17], "ha_info": 15, "had": [13, 17], "half_dataset": 10, "handi": 13, "handl": [3, 6, 13, 14], "handler": 13, "happen": [9, 13], "happi": 4, "harri": [0, 13], "harvest": 13, "hash": 16, "have": [0, 4, 5, 7, 8, 10, 11, 13, 14, 15, 16, 17], "hdf5": [10, 16], "hdf5_plugin": 10, "hdr": 13, "hdr_in": 13, "hdr_out": 13, "head": 17, "header": [5, 9, 13, 15, 17], "heavi": [5, 13], "heidelberg": 4, "heirarchi": 17, "help": [0, 5, 9, 10, 11, 13, 17], "helpfulli": 13, "here": [4, 5, 7, 10, 12, 13, 14, 15, 16], "hierarchi": [10, 17], "hierarchy_level": 17, "high": [7, 13, 14, 15], "higher": [14, 17], "highli": 13, "histori": 13, "hit": [12, 17], "hkl2000": 1, "holder": 8, "home": [12, 13], "hope": 13, "hopefulli": 11, "horribl": 13, "horribli": 13, "how": [2, 5, 9, 14, 15, 16, 17], "howev": [1, 2, 3, 5, 6, 8, 9, 10, 13, 15, 16, 17], "href": 13, "html": [4, 13, 14], "htpx": [0, 1, 13], "http": [3, 4, 13], "hunt": 13, "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "i02": [7, 15], "i19": 13, "i222": 13, "ic": 13, "id": 17, "idea": 13, "ideal": [7, 9], "identif": 13, "identifi": 13, "idxref": 13, "ignor": [9, 13], "ii": 13, "illustr": 5, "imag": [1, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17], "image1": 16, "image2": 16, "image3": 16, "image_": 16, "image_001": 7, "image_mast": 14, "image_view": 17, "images_to_us": 17, "img": [5, 7, 10, 15], "immedi": 11, "implement": 13, "impli": 8, "import": [13, 14, 15, 17], "imposs": [0, 1], "improv": [13, 14, 17], "in_spindle_plan": 17, "incident": 8, "includ": [3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17], "inclus": [10, 13], "incomplet": 13, "incorrect": [7, 13], "incorrectli": [13, 17], "inde": 13, "index": [9, 10, 11, 12, 13, 14, 15, 16, 17], "indic": [9, 11, 13, 15, 16], "indirect": 8, "individu": [9, 13, 14], "infer": 9, "infl": 13, "inform": [5, 11, 13, 14], "infrastructur": 16, "init": 10, "initi": [1, 3, 6, 7, 14, 17], "inpsect": 17, "input": [1, 3, 5, 6, 10, 13, 14, 15, 16, 17], "inspect": [14, 16], "instal": 13, "instanc": 14, "instead": [10, 13, 14, 17], "instruct": [4, 15], "instrument": 13, "insulin": 13, "insulin_1_001": 5, "integr": [10, 11, 13, 15, 16, 17], "integrat": 13, "intel": 13, "intellig": 13, "intend": 16, "intens": [1, 14], "interact": 13, "interchang": 10, "interest": 13, "interfac": 13, "intern": 7, "interpret": 17, "interrupt": 8, "invers": 9, "invert": 13, "investig": 7, "invit": 8, "io": 4, "isigma": [10, 13], "isomorph": 13, "ispyb": 13, "issu": [7, 13, 17], "item": 16, "its": [8, 17], "itself": 0, "iv": 13, "j": 0, "job": [7, 9, 14, 16], "john": 5, "join": 8, "joint": [0, 14, 17], "journal": 2, "jovin": 13, "json": 17, "june": 13, "just": [1, 5, 9, 12, 13, 17], "k5_m1s3_3_001": [7, 15], "k_sol": 14, "kabsch": [0, 1], "kai": [0, 13], "keep": [10, 17], "keep_all_reflect": 10, "keep_outli": 10, "kei": 11, "keyword": 13, "kind": 13, "known": [9, 13, 14, 17], "kunstlev": 0, "lab": [13, 17], "label": 10, "labelit": 13, "land": 13, "languag": 10, "larg": [4, 9, 13], "larger": 13, "last": [3, 6, 13], "later": [3, 6, 13, 15], "latest": [4, 5, 13], "latter": [7, 13], "lattic": [11, 13, 14], "layout": 5, "lbfgscurv": 17, "lead": 9, "least": [14, 17], "leav": 17, "legend": 11, "length": 16, "lesli": [0, 1], "less": [9, 13], "letter": 5, "level": [1, 14, 17], "levmar": 17, "liabil": 8, "liabl": 8, "librari": 13, "licenc": 0, "licens": [0, 13], "ligand": 7, "light": [0, 7, 8, 13], "like": [0, 7, 11, 12, 13, 15], "limit": [7, 8, 9, 13, 14], "line": [5, 7, 9, 10, 13, 15, 17], "link": [5, 14, 17], "list": [3, 5, 8, 10, 13, 14], "littl": [3, 6, 13], "ll": 12, "load": [5, 11], "local": 13, "locat": [13, 14, 16, 17], "log": [11, 13, 17], "logfil": [11, 13], "loggraph": 13, "long": [10, 13], "longer": [13, 17], "look": [5, 11, 13], "loss": 8, "lot": 13, "low": [7, 9, 11, 13, 15, 17], "lower": [13, 17], "lowest": [9, 11], "lp": 13, "lrem": 13, "lt": 13, "luca": 13, "lyso": 14, "lyso_1_": 14, "lyso_1_001": 14, "lyso_1_900": 14, "mac": 13, "machin": [1, 9], "macromolecular": 1, "mad": [5, 13], "made": [0, 5, 7, 13, 16], "mai": [3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 17], "mail": [3, 8], "main": [1, 13], "maintain": 13, "major": [0, 13], "make": [1, 4, 8, 9, 13], "manag": 17, "mangl": 13, "mani": [5, 9, 11, 13, 17], "manner": [10, 15, 16], "manual": [1, 7, 11, 12, 15, 17], "map": 13, "mar": 13, "mark": 13, "mask": [13, 14], "massiv": 13, "match": [9, 13, 14, 16], "materi": 8, "matrix": 13, "matter": 5, "matur": [1, 13], "max": 13, "max_cell_estim": 10, "max_lattic": 14, "max_wedge_s": 10, "max_wedge_size_degre": 10, "maximum": 13, "mc": 11, "mcd": 17, "mean": [10, 13], "meant": 13, "measur": [5, 13, 16], "mechan": [5, 13], "media": 5, "mend": 13, "mention": 15, "merchant": 8, "merg": [5, 7, 9, 13, 15], "merge2cbf": 10, "merge_bi": 16, "messag": [9, 13, 17], "met": 8, "meta2": 16, "metadata": [13, 14, 17], "method": 10, "microcryst": 13, "migrat": 13, "migrate_data": 13, "miller": 15, "millimet": 17, "min": 13, "min_imag": 13, "mini": 13, "minim": 14, "misigma": [10, 13], "misigma_fractional_loss": 10, "misinterpret": 13, "miss": 13, "mix": 2, "mm": [5, 17], "mmcif": 10, "mn": 13, "mode": [9, 13], "model": [7, 13, 14, 17], "modern": 17, "modest": 13, "modi": 0, "modif": 8, "modifi": [10, 17], "modulo": 16, "molecul": [2, 10, 13], "moment": [5, 13], "monash": 13, "monoclin": 13, "monom": 5, "more": [0, 2, 5, 7, 9, 10, 13, 14, 15, 16, 17], "mosaic": [11, 13], "mosflm": [0, 1, 5, 13], "mosflm_beam_centr": 5, "most": [0, 1, 3, 6, 7, 13, 14, 15, 16, 17], "mostli": 11, "motiv": [1, 17], "move": [10, 13, 16], "mp": 11, "mpg": 4, "mpimf": 4, "mtz": [13, 14, 15, 16], "mtzdump": 13, "much": [0, 7, 13], "multi": [1, 3, 6, 13, 14], "multipl": [7, 9, 10, 13, 14, 16, 17], "multiprocess": [9, 10], "must": [2, 8, 14, 16, 17], "mutant": 13, "mx": [1, 3, 6], "mx1234": [7, 15], "my": [5, 7, 12, 13, 15], "n": [13, 16], "n_crystal": [14, 17], "name": [5, 8, 11, 13, 16], "narrow": 13, "nasti": 13, "nativ": [5, 9, 13], "necessari": [0, 14, 17], "need": [1, 4, 5, 7, 9, 10, 12, 13, 16, 17], "neg": [13, 17], "neglig": 8, "neither": [8, 17], "neq": [10, 12, 15], "net": 3, "never": 13, "new": [1, 3, 6], "next": 16, "nice": [7, 11], "nick": 0, "njob": [9, 13], "nnnn": 13, "noir1": 13, "non": [13, 17], "nonchir": 10, "none": [10, 17], "nonsens": 13, "nor": 8, "normal": [9, 17], "note": [14, 16, 17], "notic": 8, "novic": [3, 6], "now": [4, 9, 10, 13], "nproc": [5, 9, 10, 13, 14], "nref": 17, "null": 17, "number": [5, 7, 9, 10, 13, 14, 16], "numer": [0, 13], "o": 11, "object": 15, "observ": [7, 17], "obtain": [4, 8, 9, 17], "oc": 11, "occasion": 13, "off": 13, "offset": 13, "often": [1, 2, 13], "oh": 13, "ok": 11, "old": 13, "omit": 14, "onc": [4, 13, 17], "one": [5, 9, 10, 11, 13, 14, 15, 16, 17], "ongo": [7, 13], "onli": [4, 5, 7, 9, 11, 13, 14, 16, 17], "onward": 14, "ooo": 11, "ooooooo": 11, "oooooooo": 11, "ooooooooo": 11, "oooooooooo": 11, "ooooooooooooo": 11, "ooooooooooooooooooo": 11, "oooooooooooooooooooo": 11, "ooooooooooooooooooooooo": 11, "oooooooooooooooooooooooo": 11, "ooooooooooooooooooooooooooooooooooo": 11, "ooooooooooooooooooooooooooooooooooooooo": 11, "oooooooooooooooooooooooooooooooooooooooooooooo": 11, "ooooooooooooooooooooooooooooooooooooooooooooooooooo": 11, "oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo": 11, "op": 11, "open": 0, "oper": [7, 13], "opinion": [3, 6], "optimis": 13, "option": [2, 4, 5, 12, 13, 14, 15, 17], "order": [4, 5, 14], "organis": 15, "orient": [13, 17], "origin": [13, 17], "orthorhomb": 13, "other": [5, 8, 9, 13, 14, 17], "otherwis": [8, 13], "out": [5, 8, 13], "out_spindle_plan": 17, "outcom": [2, 10], "outer": 7, "outlier": [10, 17], "output": [2, 3, 6, 10, 13, 14, 16], "over": 13, "overal": [11, 14], "overload": [11, 13], "overrid": 13, "overridden": 10, "owner": 8, "p1": 17, "p2": 13, "p21": 10, "p222": 13, "p422": 10, "p43212": 14, "packag": [0, 1, 3, 6, 13], "page": 13, "pair": [5, 10, 12, 13, 15], "panel": 14, "panic": 10, "parallel": [13, 14], "parallelis": 13, "param": 10, "paramat": 7, "paramet": [9, 13, 14, 17], "parameteris": 17, "part": [1, 4, 7, 14, 17], "partial": 13, "particular": [8, 16], "particularli": [0, 9], "pass": [3, 6, 9, 10, 13, 15], "path": [4, 5, 7, 9, 10, 13, 14, 16], "pc": 13, "pdb": 14, "peak": [10, 12, 13, 15], "penalti": 11, "peopl": [3, 6, 10], "per": [5, 9, 11, 13, 17], "percent": 13, "perform": [3, 6, 13, 14, 15, 17], "perhap": 13, "permiss": [8, 13], "permit": 8, "permut": 13, "perpendicular": 17, "perri": 13, "pharmaceut": [3, 6], "phase": [7, 13], "phenix": 13, "phi": 13, "phi_step": 10, "phil": [0, 13, 14, 17], "photon": 17, "physic": 17, "pick": 13, "pilatu": [11, 13], "pipelin": [2, 4, 5, 7, 9, 10, 12, 13, 14, 15, 17], "pixel": [13, 17], "place": [5, 13], "plain": [13, 17], "plan": 13, "plane": 17, "plate": 13, "pleas": [2, 3, 6, 8, 10, 13], "plot": 13, "plu": 14, "plugin": 10, "point": [13, 16], "pointgroup": [7, 13], "pointless": [0, 10, 13], "polar": 13, "polish": 13, "polycryst": 13, "poor": 7, "popul": 14, "portal": 13, "posit": 17, "possibl": [8, 11, 13, 14, 15, 16, 17], "postrefin": 13, "powel": [0, 13], "power": [9, 13], "ppc": 13, "prcoess": 16, "preceed": 17, "predict": 17, "prefer": [13, 14, 17], "prepar": 13, "present": [5, 14], "previou": 13, "previous": [13, 17], "primarili": [2, 13], "primit": 13, "print": [3, 6, 13], "printhead": 13, "printpeak": 13, "prior": 8, "probabl": [5, 13], "problem": [3, 4, 6, 13, 14], "procedur": 4, "process": [3, 5, 6, 7, 10, 11, 13, 15, 16, 17], "processor": [5, 9, 13], "procur": 8, "produc": [13, 16], "product": [0, 8], "profil": 13, "profile_grid_s": 13, "profit": 8, "program": [0, 1, 2, 3, 6, 7, 13, 14, 15, 17], "project": [0, 1, 5, 9, 10, 13, 15], "project_crystal_fre": 13, "promot": 8, "prone": 17, "properli": [8, 13], "propog": 13, "prove": [3, 6], "provid": [3, 5, 6, 8, 9, 13, 14, 16, 17], "pseudo": 13, "ptovid": 13, "public": 17, "publish": [0, 3, 6, 8], "pull": 13, "pun": 13, "purpos": 8, "put": 13, "px": 17, "py": 13, "pycbf": 13, "python": [10, 13], "pythondriv": 13, "q": 9, "qsub": 9, "qsub_command": 9, "qualiti": [2, 7, 14], "quantum": 13, "question": 2, "queue": 9, "quick": [13, 14, 15], "r": [0, 13], "r3": 13, "radiat": [7, 13], "rai": [3, 6, 13], "rais": 13, "ralf": 0, "rang": [7, 10, 13, 17], "rare": 13, "raster": 13, "rate": [14, 17], "rather": [2, 9, 13], "raw": 0, "raxi": 13, "rd": 13, "reach": 1, "reachabl": 13, "read": [9, 10, 11, 12, 13, 15, 17], "read_all_image_head": 9, "readabl": 13, "real": 7, "real_space_grid_search": 10, "realli": 5, "reason": [7, 9, 13, 17], "rebatch": 13, "recent": [0, 13], "recip": 10, "recognis": 13, "recommend": [4, 13, 14], "record": [7, 11, 13], "recycl": 13, "redistribut": 8, "reduc": [1, 5, 13, 14, 16], "reduct": [1, 13], "reduction_batch_s": 14, "redund": 13, "refactor": 13, "refer": [3, 6, 10, 13, 14, 16, 17], "reference_geometri": [14, 17], "reference_reflection_fil": 13, "refin": [1, 13], "refineri": 17, "refl": [14, 16, 17], "reflect": [13, 16, 17], "reflections_per_bin": 10, "regard": 17, "region": [13, 17], "regular": 13, "reindex": [13, 14], "reject": 17, "rel": 17, "relat": [13, 16], "relax": [13, 14], "reli": [0, 13], "reliabl": [0, 13], "remacl": 13, "remain": 17, "rememb": [2, 12, 13, 17], "remerg": [13, 14], "remind": [8, 17], "remot": [3, 6], "remov": 17, "renam": 13, "repair": 13, "repeat": [16, 17], "replac": [13, 16], "report": [2, 11, 13, 17], "repositori": 13, "represent": 11, "reproduc": [3, 6, 8], "requir": [1, 2, 13, 14, 16, 17], "rerun": [7, 15, 17], "research": 7, "reserv": 8, "reset": 13, "residu": [5, 17], "resolut": [7, 13, 14, 16], "resolution": 13, "resolv": 13, "respect": [13, 17], "respons": [8, 13], "rest": [9, 12, 17], "restraint": 14, "result": [1, 7, 11, 13, 16, 17], "retain": 8, "retir": 13, "revers": 13, "reverse_phi": 5, "reversephi": 13, "review": 13, "richard": 13, "rigaku": 13, "right": 8, "ring": 13, "rip": 5, "rise": 13, "rmea": 7, "rmerg": [7, 13], "rmsd": [11, 17], "rmsd_deltapsi": 17, "rmsd_x": 17, "rmsd_y": 17, "robust": 13, "rotat": 17, "round": [13, 17], "rpim": 7, "run": [2, 5, 9, 10, 11, 13, 14, 15, 17], "runtimeerror": 13, "sad": [5, 15], "sai": [5, 13], "same": [1, 3, 5, 6, 7, 9, 10, 11, 13, 14, 17], "sampl": [13, 17], "satisfactori": 11, "saturn": 13, "sauter": 0, "sauter_poon": 17, "sauterpoon": 17, "scala": [0, 1], "scale": [1, 5, 7, 9, 10, 12, 13, 14, 15], "scalepack": 13, "scaler": 13, "scan": [5, 10, 13, 15], "scatter": 13, "scheme": 13, "scienc": 1, "scientist": [3, 6], "screen": [11, 13], "script": [4, 10, 13, 16], "sd": 13, "sdcorrect": 13, "se": [5, 13], "search": [9, 13, 14], "second": [3, 6, 17], "secondari": 13, "section": [16, 17], "see": [10, 13, 14, 17], "seem": 7, "seen": [7, 17], "select": [5, 13], "self": 11, "semet": 5, "send": [4, 11], "sensibl": [1, 5, 7, 12], "sensibli": [11, 13], "sent": 13, "separ": [5, 10, 12, 13, 14, 15, 16], "sequenc": [5, 13, 14, 16], "sequenti": [9, 16], "seri": 14, "serial": [9, 13, 16, 17], "serious": 13, "serv": 1, "servic": 8, "set": [3, 5, 6, 7, 9, 10, 11, 14], "setup": [4, 13], "sever": [13, 17], "sfcheck": 13, "sg": 10, "sh": 4, "shall": 8, "share": 10, "shell": 7, "shift": 17, "shortli": [0, 11], "should": [4, 5, 9, 10, 11, 13, 14, 16, 17], "show": [15, 16, 17], "shown": [7, 11, 15, 16, 17], "side": 13, "sigma": [7, 13], "sigma_tau": 10, "sign": 13, "signal": [13, 17], "signific": 13, "significantli": 17, "sim_mx": 13, "similar": [13, 16], "simpl": 5, "simplelbfg": 17, "simpli": [2, 4, 13, 15, 17], "simul": 13, "simultan": 9, "singl": [5, 7, 9, 13, 17], "situat": 9, "size": [13, 14], "skip": 9, "slice": 13, "slight": 17, "slightli": 13, "slope": 7, "slow": 17, "slow_axi": 17, "small": [2, 10, 13], "small_molecul": [2, 10], "smaller": 13, "smart": 13, "smarter": 13, "so": [2, 10, 13, 17], "softwar": [0, 1, 3, 6, 8, 13, 16], "solut": [1, 11, 13, 17], "solv": 8, "solvent": [5, 14], "some": [1, 5, 9, 10, 11, 12, 13, 14, 17], "someth": [5, 7, 12, 13], "sometim": [9, 13, 17], "sorri": 13, "sort": 13, "sourc": [0, 3, 4, 7, 8, 13], "sourceforg": 3, "space": [2, 9, 13, 14], "space_group": [5, 9, 10, 14, 17], "spacegroup": [10, 13], "sparselevmar": 17, "special": 8, "specif": [3, 6, 8, 10, 13, 16, 17], "specifi": [9, 10, 13, 14, 15, 16, 17], "speed": 13, "speedup": 9, "split": [13, 16], "spot": [12, 13, 17], "spotfind": [14, 17], "spread": [11, 13], "squash": 13, "sr": 5, "ssx_index": 17, "ssx_reduc": [14, 16], "stack": 13, "stage": 13, "stamp": 13, "standard": [4, 13, 16], "start": [7, 9, 10, 13, 14, 15, 17], "start_end": [5, 9, 15], "starting_geometri": 17, "statist": [7, 13], "statu": 11, "step": [9, 13, 14, 16, 17], "stepwis": 14, "still": [5, 13, 17], "stop": 9, "store": 16, "straightforward": [0, 7, 17], "strang": 13, "strategi": 13, "streamlin": 1, "strength": 17, "strict": [8, 16], "structur": [0, 1, 7, 8, 14, 16], "style": [10, 13], "subdirectori": 13, "subfold": 16, "submit": 9, "subsequ": 16, "subset": [5, 7], "substanti": 13, "substitut": 8, "subtl": 13, "success": [14, 17], "successfulli": [9, 13, 14, 17], "suffer": 17, "suffici": [1, 17], "suggest": [13, 14], "suit": [9, 10, 13], "suitabl": [13, 14, 17], "summari": 13, "support": [0, 3, 4, 6, 9, 11, 13, 14, 16], "sure": 4, "surpris": 13, "svn": 13, "sweep": [5, 7, 9, 13, 15], "sweep1": [9, 11, 15], "sweep2": 9, "sweep_1_0001": 9, "sweep_2_0001": 9, "switch": 13, "symmetri": [9, 10, 13, 14], "symptom": 17, "synchrotron": [1, 3, 6, 13], "syntax": 7, "system": [3, 6, 13], "t": [5, 9, 10, 12, 13], "tabl": [13, 14], "tackl": 14, "take": [9, 13, 14], "taken": [9, 14], "tar": 5, "target": 9, "task": 13, "tau1": 17, "techniqu": 1, "tell": [9, 10, 12, 13, 15], "templat": [9, 13, 14, 16], "temporari": 13, "temporarili": [13, 17], "term": [1, 15], "termin": 4, "test": [0, 3, 5, 6, 13], "text": [5, 13, 17], "tg6623": 13, "th": 5, "than": [2, 5, 9, 13, 16, 17], "thank": [0, 5, 8, 13], "thaumatin": 11, "thei": [0, 5, 13, 16, 17], "them": [3, 6, 9, 13, 17], "theori": 8, "therefor": [0, 1, 4, 7, 17], "therein": 13, "theta": 13, "thi": [0, 1, 2, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "thing": [5, 13], "think": 13, "those": [7, 9, 13], "though": [2, 5, 7, 13], "three": [13, 17], "threshold": [13, 14], "through": [0, 7, 13, 14], "thu": 16, "tidi": [10, 13], "tild": 13, "tile": 13, "time": [1, 2, 5, 7, 9, 10, 13, 14], "tmp": 13, "togeth": [9, 13, 15, 17], "token": 13, "told": [1, 13], "toler": 16, "too": [13, 17], "tool": [1, 13, 17], "top": 17, "tort": 8, "total": [7, 9], "toward": [10, 17], "tp": 11, "trace": 13, "traceback": 13, "track": 13, "translat": 17, "trap": 13, "trek": 1, "tricki": 13, "trickier": 14, "trigger": 16, "trigon": 13, "trim": 13, "true": [2, 4, 5, 9, 10, 14], "truncat": 13, "trust": 0, "trust_beam_centr": 9, "trust_timestamp": 13, "trusted_region": 13, "try": [2, 12, 13], "tukei": 17, "twin": 13, "two": [5, 11, 13], "type": [5, 9, 13], "typic": [13, 14, 17], "ub": 13, "uk": [0, 1, 3, 4], "ultim": 15, "uncom": 5, "under": [0, 8], "underli": 17, "understand": [9, 13], "understood": [11, 15], "unhappi": 13, "unhelp": 13, "uniformli": 13, "uniqu": [7, 15], "unit": [9, 11, 13, 14, 15], "unit_cel": [5, 9, 10, 14, 17], "univers": 13, "unix": 5, "unknown": 13, "unless": 13, "unmerg": 13, "unread": 13, "unrol": 13, "unstabl": 13, "until": [13, 14, 17], "unusu": [7, 11, 13], "up": [4, 7, 9, 11, 13], "updat": 13, "upon": [8, 14], "us": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 17], "usag": [3, 6, 12, 13, 15], "user": [0, 1, 2, 3, 6, 8, 13, 14, 16], "user_cel": 13, "user_resolut": 13, "usual": [5, 7, 11], "utilis": 9, "v": 13, "valid": 16, "valu": [5, 13, 14, 16, 17], "variabl": 13, "variat": 13, "varieti": 16, "vector": 13, "veri": [5, 7, 13, 17], "verifi": 16, "version": [11, 13], "via": [5, 9, 13], "view": 17, "viewer": 14, "viru": 13, "viz": 13, "w": [0, 1], "wa": [1, 3, 5, 6, 7, 13, 17], "wai": [4, 5, 7, 8, 10, 13, 16, 17], "wait": 13, "want": [5, 10, 12, 13], "warn": [10, 13], "warranti": 8, "wast": [1, 13], "waterman": 13, "wavelength": [3, 5, 6, 9, 13, 15, 17], "we": [7, 9, 10, 17], "weaker": 11, "web": 13, "wedg": 13, "weird": 13, "well": [1, 5, 12, 13, 16, 17], "were": [1, 5, 7, 10, 13, 16, 17], "what": [5, 13, 17], "when": [1, 7, 9, 13, 14, 17], "where": [9, 11, 13, 16, 17], "whether": 8, "which": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17], "whichev": 13, "while": [7, 11, 13, 17], "who": 8, "whole": [7, 17], "wide": 16, "wilson": [7, 13], "win32": 13, "window": [5, 13], "winter": [0, 2, 8], "wish": [3, 5, 6, 7, 9], "within": [10, 14, 17], "without": [0, 5, 8, 13, 14], "wolfgang": 0, "work": [2, 3, 4, 6, 7, 13], "worth": [4, 13], "worthwhil": 2, "would": [0, 2, 7, 13, 15, 16, 17], "write": [13, 16], "write_xinfo": 13, "written": [3, 6, 8, 11, 15], "wrong": [5, 7, 13], "ws050": 13, "www": 4, "x": [3, 5, 6, 10, 12, 13, 15, 17], "x77788": 13, "xd": [0, 1, 4, 5, 8, 10, 12, 15], "xdsintegrat": 13, "xdsintegraterr": 13, "xia": 13, "xia2": [0, 1, 2, 3, 4, 5, 6, 7, 10, 12, 13, 17], "xia2_ccp4_61": 13, "xia2_ssx": 14, "xia2_ssx_reduc": 14, "xia2bb": 8, "xia2ccp4i": 13, "xia2cor": 13, "xia2html": [11, 13], "xia2setup": [5, 13], "xinfo": [5, 9, 10, 13], "xml": 13, "xparallel": [4, 13], "xparm": 13, "xparm_ub": 13, "xscale": [5, 10, 12, 13, 15], "xxx": 5, "xyz": 17, "y": [5, 17], "yaml": 16, "year": 13, "yml": 14, "you": [3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15], "your": [2, 3, 4, 5, 6, 9, 10, 11, 13], "yourself": 2, "z": [5, 17], "zip": 5, "\u03b1": 10, "\u03b2": 10, "\u03b3": 10}, "titles": ["Acknowledgements", "Background", "Comments", "Introduction", "Installation", "Insulin tutorial", "Introduction", "Introductory example", "xia2 license", "Processing multi-crystal datasets with xia2", "Parameters", "Program output", "Quick start guide", "Release notes", "Processing serial synchrotron crystallography (SSX) datasets with xia2", "Using xia2", "Merging SSX data in groups with xia2", "Overcoming problems with the detector geometry for SSX data"], "titleterms": {"0": 13, "1": 13, "2": 13, "3": 13, "4": 13, "5": 13, "6": 13, "7": 13, "8": 13, "acknowledg": 0, "ad": 13, "add": 13, "background": 1, "beam": 17, "big": 13, "bold": 13, "bug": 13, "cc": 13, "ccp4": 13, "centr": 17, "chang": 13, "comment": 2, "commonli": 10, "contact": 3, "cope": 13, "crystal": 9, "crystallographi": 14, "data": [9, 13, 14, 16, 17], "dataset": [9, 14], "deal": 13, "detector": 17, "dial": 13, "difficulti": 14, "distanc": 17, "dose": 16, "dose_series_repeat": 16, "etc": 13, "exampl": 7, "file": 16, "fix": 13, "generalis": 16, "geometri": [14, 17], "group": [14, 16], "guid": 12, "half": 13, "html": 11, "huge": 13, "input": 7, "instal": 4, "insulin": 5, "integr": 14, "introduct": [3, 6], "introductori": 7, "licens": 8, "limit": 10, "merg": [14, 16], "metadata": 16, "modifi": 7, "mostli": 13, "multi": [9, 17], "new": 13, "note": 13, "option": [10, 16], "output": 11, "overcom": [14, 17], "page": 11, "panel": 17, "parallel": 9, "paramet": 10, "patch": 13, "phil": 10, "problem": 17, "process": [9, 14], "program": [10, 11], "quick": 12, "reduct": 14, "refin": [14, 17], "relax": 17, "releas": 13, "remov": 13, "resolut": 10, "restraint": 17, "scala": 13, "seri": 16, "serial": 14, "set": [13, 17], "sinc": 13, "ssx": [14, 16, 17], "start": 12, "synchrotron": 14, "tutori": 5, "txt": 11, "us": [10, 15, 16], "xd": 13, "xia2": [8, 9, 11, 14, 15, 16], "yml": 16}})