!***************************************************************************** ! Example file XDS.INP for Pilatus detector at CHESS ! Characters in a line to the right of an exclamation mark are comment. !***************************************************************************** ! !Standard settings for the detector that rarely need to be changed DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=2000000000 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 TRUSTED_REGION=0.0 1.15 !Relative radii limiting trusted detector region SENSOR_THICKNESS=1.000 UNTRUSTED_RECTANGLE= 487 495 1 2527 ! these do not have to be specified UNTRUSTED_RECTANGLE= 981 989 1 2527 ! but it is better UNTRUSTED_RECTANGLE=1475 1483 1 2527 ! ... UNTRUSTED_RECTANGLE=1969 1977 1 2527 ! painstakingly checked KD 2012-01-14 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_ELLIPSE= 910 1110 1010 1210 ! ellipse enclosed by X1 X2 Y1 Y2 !MAXIMUM_NUMBER_OF_JOBS=4 !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster !MAXIMUM_NUMBER_OF_PROCESSORS=4!<33;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 !NX=number of fast pixels (along X); QX=length of a 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 !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default !====================== JOB CONTROL PARAMETERS =============================== JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT ! JOB= COLSPOT IDXREF DEFPIX XPLAN ! INTEGRATE CORRECT ! JOB= IDXREF DEFPIX XPLAN ! INTEGRATE CORRECT ! JOB= XYCORR INIT DEFPIX INTEGRATE CORRECT ! JOB= DEFPIX INTEGRATE CORRECT ! JOB= INTEGRATE CORRECT ! JOB= CORRECT !====================== GEOMETRICAL PARAMETERS =============================== !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 ! ! ***** You will have to edit the following two parameter lines ***** ! ! Detector origin, i.e. beam position (pixels). ! Use (X/pixsize),(npix-(Y/pixsize)); X,Y from ADX mm coords, ! equivalent to (Y/pixsize),(X/pixsize); X,Y from denzo or mosflm ORGX=1188.0 ORGY=1229.0 DETECTOR_DISTANCE= 700.0 !(mm) ! ! Rotation axis is currently along -X at all MacCHESS stations. ! ROTATION_AXIS= -1.0 0.0 0.0 ! A1, F1, F2, F3 OSCILLATION_RANGE=0.5 ! degrees (>0) *** Edit this *** ! X-RAY_WAVELENGTH=0.6306 ! Angstroem, A1 as of September 2015 X-RAY_WAVELENGTH=0.9769 ! Angstroem, F1 as of September 2015 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !======================= CRYSTAL PARAMETERS ================================= ! *** Edit for your system *** SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. UNIT_CELL_CONSTANTS= 90.396 90.396 45.466 90 90 120 ! 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. !==================== SELECTION OF DATA IMAGES ============================== !Generic file name and format (optional) of data images ! ! ***** Edit for your data ***** ! NAME_TEMPLATE_OF_DATA_FRAMES=../abc_1_???.cbf ! CBF is usual format for Pilatus DATA_RANGE=1 360 !Numbers of first and last data image collected BACKGROUND_RANGE=1 6 !Numbers of first and last data image for background SPOT_RANGE=1 5 !First and last data image number for finding spots SPOT_RANGE=7 10 !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 !REFERENCE_DATA_SET= CK.HKL !Name of a reference data set (optional) !====================== 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=6.0 CLUSTER_RADIUS=3 !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 ======================= ! For newer XDS, use POSITION instead of DISTANCE in following !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= 6000 30000 !Used by DEFPIX !for excluding shaded parts of the detector. INCLUDE_RESOLUTION_RANGE=30.0 0.0 !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=0.15 !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 data images !Suggested values are listed near the end of INTEGRATE.LP !BEAM_DIVERGENCE= 0.473 !arctan(spot diameter/DETECTOR_DISTANCE) !BEAM_DIVERGENCE_E.S.D.= 0.047 !half-width (Sigma) of BEAM_DIVERGENCE !REFLECTING_RANGE= 1.100 !for crossing the Ewald sphere on shortest route !REFLECTING_RANGE_E.S.D.= 0.169 !half-width (mosaicity) of REFLECTING_RANGE !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=9 !used by: INTEGRATE !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9 !used by: INTEGRATE !CUT=2.0 !defines the integration region for profile fitting !MINPK=75.0 !minimum required percentage of observed reflection intensity !DELPHI= 5.0!controls the number of reference profiles and scaling factors !======= 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=6 !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=6 !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