!******************************************************************************** ! ! # # ### ##### ##### # ! ! # # # # # # # # # # ! ! # # # # # # # # ! ! # # # ###### ##### # # ! ! # # # # # # # ####### ! ! # # # # # # # # # # ! ! # # ### ##### ##### # # ! ! ! ! ! ! Example file XDS.INP for the PILATUS 6M pixel detector at Beamline X06SA at SLS ! ! ! ! Last edit: justyna wojdyla, 2015/03/06 ! !*********************************************************************************! !---------------------------------------------------------------------------------! !---------------------- START REDUCED PARAMETER SECTION --------------------------! !---------------------------------------------------------------------------------! !====================== JOB CONTROL PARAMETERS =============================== JOB= ALL !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !====================== GEOMETRICAL PARAMETERS =============================== ORGX=1161 ORGY=1261.0 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 DETECTOR_DISTANCE= 300.0 !(mm) OSCILLATION_RANGE=0.025 !degrees (>0vi ) X-RAY_WAVELENGTH=1.0000 !Angstroem !======================= CRYSTAL PARAMETERS ================================= SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. UNIT_CELL_CONSTANTS= 77.7 77.7 77.7 90 90 90 !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0 !==================== SELECTION OF DATA IMAGES ============================== NAME_TEMPLATE_OF_DATA_FRAMES=../testshot_1_0????.cbf CBF DATA_RANGE=1 3600 !Numbers of first and last data image collected BACKGROUND_RANGE=1 10 !Numbers of first and last data image for background SPOT_RANGE=1 360 !First and last data image number for finding spots !================= PARAMETERS CONTROLLING REFINEMENTS ======================= REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !DISTANCE REFINE(INTEGRATE)=POSITION DISTANCE BEAM ORIENTATION CELL !AXIS REFINE(CORRECT)=POSITION DISTANCE BEAM ORIENTATION CELL AXIS !====================== COMPUTING PARAMETERS ================================== !MINUTE=1 MAXIMUM_NUMBER_OF_JOBS=8 !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster MAXIMUM_NUMBER_OF_PROCESSORS=6 !<25;ignored by single cpu version of xds !---------------------------------------------------------------------------------! !---------------------- END REDUCED PARAMETER SECTION ----------------------------! !---------------------------------------------------------------------------------! !======================== DETECTOR PARAMETERS =============================== DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=1048500 SENSOR_THICKNESS=0.32 !SILICON=-1.0 !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default !NX=number of fast pixels (along X); QX=length of an X-pixel (mm) !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm) NX=2463 NY=2527 QX=0.172 QY=0.172 !PILATUS 6M !UNTRUSTED_ELLIPSE=1184 1289 1218 1322 ! ellipse enclosed by X1 X2 Y1 Y2 !UNTRUSTED_RECTANGLE= 487 495 1 2527 !UNTRUSTED_RECTANGLE= 981 989 1 2527 !UNTRUSTED_RECTANGLE=1475 1483 1 2527 !UNTRUSTED_RECTANGLE=1969 1977 1 2527 !UNTRUSTED_RECTANGLE= 1 2463 195 213 !UNTRUSTED_RECTANGLE= 1 2463 407 425 !UNTRUSTED_RECTANGLE= 1 2463 619 637 !UNTRUSTED_RECTANGLE= 1 2463 831 849 !UNTRUSTED_RECTANGLE= 1 2463 1043 1061 !UNTRUSTED_RECTANGLE= 1 2463 1255 1273 !UNTRUSTED_RECTANGLE= 1 2463 1467 1485 !UNTRUSTED_RECTANGLE= 1 2463 1679 1697 !UNTRUSTED_RECTANGLE= 1 2463 1891 1909 !UNTRUSTED_RECTANGLE= 1 2463 2103 2121 !UNTRUSTED_RECTANGLE= 1 2463 2315 2333 !UNTRUSTED_QUADRILATERAL=565 574 1519 1552 1508 1533 566 1536 !MINIMUM_FRACTION_OF_BACKGROUND_REGION=0.01 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ! 0.0 cos(2theta) sin(2theta) TRUSTED_REGION=0.0 1.15 !Relative radii limiting trusted detector region !MAXIMUM_NUMBER_OF_JOBS=8 !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster !MAXIMUM_NUMBER_OF_PROCESSORS=6!<32;ignored by single cpu version of xds !SECONDS=0 !Maximum number of seconds to wait until data image must appear !TEST=1 !Test flag. 1,2 additional diagnostics and images !====================== JOB CONTROL PARAMETERS =============================== !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !====================== GEOMETRICAL PARAMETERS =============================== !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 !ORGX=1232.0 ORGY=1314.0 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 !DETECTOR_DISTANCE= 204.0 !(mm) ROTATION_AXIS= 1.0 0.0 0.0 ! Optimal choice is 0.5*mosaicity (REFLECTING_RANGE_E.S.D.= mosaicity) ! The detector can measure at 25Hz frame rate; take the advantage of fine ! phi-slicing datacollection: Müller, Wang and Schulze-Briese (2012), Acta Cryst D68, 42 !OSCILLATION_RANGE=0.1 !degrees (>0) !X-RAY_WAVELENGTH=1.000 !Angstroem INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.99 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !======================= CRYSTAL PARAMETERS ================================= !SPACE_GROUP_NUMBER=196 !0 for unknown crystals; cell constants are ignored. !UNIT_CELL_CONSTANTS= 180.7 180.7 180.7 90 90.0 90.0 ! You may specify here the x,y,z components for the unit cell vectors if ! known from a previous run using the same crystal in the same orientation !UNIT_CELL_A-AXIS= !UNIT_CELL_B-AXIS= !UNIT_CELL_C-AXIS= !Optional reindexing transformation to apply on reflection indices !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0 !FRIEDEL'S_LAW=FALSE !Default is TRUE. !REFERENCE_DATA_SET= CK.HKL !Name of a reference data set (optional) !==================== SELECTION OF DATA IMAGES ============================== !Generic file name and format (optional) of data images !NAME_TEMPLATE_OF_DATA_FRAMES=../images/ferritin_1_0????.cbf !CBF !DATA_RANGE=1 60 !Numbers of first and last data image collected !BACKGROUND_RANGE=1 6 !Numbers of first and last data image for background !SPOT_RANGE=1 60 !First and last data image number for finding spots !==================== DATA COLLECTION STRATEGY (XPLAN) ====================== ! !!! Warning !!! ! If you processed your data for a crystal with unknown cell constants and ! space group symmetry, XPLAN will report the results for space group P1. !STARTING_ANGLE= 0.0 STARTING_FRAME=1 !used to define the angular origin about the rotation axis. !Default: STARTING_ANGLE= 0 at STARTING_FRAME=first data image !RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2 !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES=30.0 120 15 !====================== INDEXING PARAMETERS ================================= !Never forget to check this, since the default 0 0 0 is almost always correct! !INDEX_ORIGIN= 0 0 0 ! used by "IDXREF" to add an index offset !Additional parameters for fine tuning that rarely need to be changed !INDEX_ERROR=0.05 INDEX_MAGNITUDE=8 INDEX_QUALITY=0.8 SEPMIN=4.0 ! default is 6 for other detectors CLUSTER_RADIUS=2 ! default is 3 for other detectors !MAXIMUM_ERROR_OF_SPOT_POSITION=3.0 !MAXIMUM_ERROR_OF_SPINDLE_POSITION=2.0 !MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.5 !============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY ============= !Decision constants for detection of lattice symmetry (IDXREF, CORRECT) MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated !Decision constants for detection of space group symmetry (CORRECT). !Resolution range for accepting reflections for space group determination in !the CORRECT step. It should cover a sufficient number of strong reflections. TEST_RESOLUTION_RANGE=8.0 4.5 MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas !================= PARAMETERS CONTROLLING REFINEMENTS ======================= !REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !DISTANCE !REFINE(INTEGRATE)=!DISTANCE BEAM ORIENTATION CELL !AXIS !REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS !================== CRITERIA FOR ACCEPTING REFLECTIONS ====================== VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 8000 30000 !Used by DEFPIX !for excluding shaded parts of the detector. INCLUDE_RESOLUTION_RANGE=50.0 1.5 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT !used by CORRECT to exclude ice-reflections !EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom !EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom !EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom !EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom !EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom !EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong !EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak !EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong !EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak !EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak !MINIMUM_ZETA=0.05 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT) !WFAC1=1.0 !This controls the number of rejected MISFITS in CORRECT; !a larger value leads to fewer rejections. !REJECT_ALIEN=20.0 ! Automatic rejection of very strong reflections !============== INTEGRATION AND PEAK PROFILE PARAMETERS ===================== !Specification of the peak profile parameters below overrides the automatic !determination from the images !Suggested values are listed near the end of INTEGRATE.LP !BEAM_DIVERGENCE= 0.80 !arctan(spot diameter/DETECTOR_DISTANCE) !BEAM_DIVERGENCE_E.S.D.= 0.080 !half-width (Sigma) of BEAM_DIVERGENCE !REFLECTING_RANGE= 0.780 !for crossing the Ewald sphere on shortest route !REFLECTING_RANGE_E.S.D.= 0.113 !half-width (mosaicity) of REFLECTING_RANGE NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13!used by: INTEGRATE !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9 !used by: INTEGRATE !DELPHI= 6.0!controls the number of reference profiles and scaling factors !CUT=2.0 !defines the integration region for profile fitting !MINPK=75.0 !minimum required percentage of observed reflection intensity !======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) ======= !MINIMUM_I/SIGMA=3.0 !minimum intensity/sigma required for scaling reflections !NBATCH=-1 !controls the number of correction factors along image numbers !REFLECTIONS/CORRECTION_FACTOR=50 !minimum #reflections/correction needed !PATCH_SHUTTER_PROBLEM=TRUE !FALSE is default !STRICT_ABSORPTION_CORRECTION=TRUE !FALSE is default !CORRECTIONS= DECAY MODULATION ABSORPTION !=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS ================= !STRONG_PIXEL=3.0 !used by: COLSPOT !A 'strong' pixel to be included in a spot must exceed the background !by more than the given multiple of standard deviations. !MAXIMUM_NUMBER_OF_STRONG_PIXELS=1500000 !used by: COLSPOT !SPOT_MAXIMUM-CENTROID=3.0 !used by: COLSPOT MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 !used by: COLSPOT !This allows to suppress spurious isolated pixels from entering the !spot list generated by "COLSPOT". !NBX=3 NBY=3 !Define a rectangle of size (2*NBX+1)*(2*NBY+1) !The variation of counts within the rectangle centered at each image pixel !is used for distinguishing between background and spot pixels. !BACKGROUND_PIXEL=6.0 !used by: COLSPOT,INTEGRATE !An image pixel does not belong to the background region if the local !pixel variation exceeds the expected variation by the given number of !standard deviations. !SIGNAL_PIXEL=3.0 !used by: INTEGRATE !A pixel above the threshold contributes to the spot centroid !FIXED_SCALE_FACTOR=TRUE !Default is FALSE; used by : INIT,INTEGRATE