!*****************************************************************************
! File XDS.INP  containing named arguments for running XDS (arbitrary order).
! For further explanations of the meaning of these parameters see 'xds.man'.
! Characters in a line to the right of an exclamation mark are comment.
!*****************************************************************************
!************* Example for RAXIS-V detector (4000 x 4000 pixels)  ************
!************* (Same geometry applies to RAXIS-II & IV images,    ************
!*************  except for opposite direction of rotation axis)   ************
!*****************************************************************************
!
!NOTE: Hi/Lo-Ratio is assumed as 32 if XDS cannot correctly interpret the
!      corresponding floating point value in the header of the images.
!NOTE: Pixel values > 262144 are always treated as OVERLOAD by XDS.
!
!*****************************************************************************

 JOB= XDS !XYCORR INIT COLSPOT IDXREF DEFPIX COLPROF PROFIT CORRECT GLOREF

!>>>>>>>>>>> Detector description for RAXIS V at the RIKEN Harima Institute
 DETECTOR=RAXIS           OVERLOAD=250000
 NX=4000 NY=4000 QX=0.1000 QY=0.100 !RAXIS-V
!NX=3000 NY=3000 QX=0.1000 QY=0.100 !RAXIS-IV
!NX=1900 NY=1900 QX=0.1017 QY=0.105 !RAXIS-II
!NX= 950 NY= 950 QX=0.2034 QY=0.210 !RAXIS-II
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0  0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 -1.0 0.0
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
 ROTATION_AXIS= 0.0 -1.0 0.0 !RAXIS-V
!ROTATION_AXIS= 0.0 1.0 0.0  !RAXIS-II & IV
 ORGX=1992.0  ORGY=1995.0    !Origin on detector (pixels)
 DETECTOR_DISTANCE=-200.0    !Signed distance of detector from crystal (mm)
 OSCILLATION_RANGE=1.0       !Of each data frame in degrees (must be >0)
 !Spindle position of crystal at beginning of data frame # STARTING_FRAME=
 STARTING_ANGLE=  0.0      STARTING_FRAME=1
 X-RAY_WAVELENGTH=1.0200         !Angstroem
 FRACTION_OF_POLARIZATION=0.990  !0.90 at DESY; 0.5 for unpolarized beam.
 POLARIZATION_PLANE_NORMAL= 1.0 0.0 0.0
 RESOLUTION_RANGE_FOR_ACCEPTING_REFLECTIONS= 20.0  0!1.8   !Angstroem
!FRIEDEL'S_LAW=FALSE          !Default is TRUE.

 BEAM_DIVERGENCE=   0.75  !arctan(spot diameter/DETECTOR_DISTANCE)
 BEAM_DIVERGENCE_E.S.D.=   0.072 !half-width (Sigma) of BEAM_DIVERGENCE=
 REFLECTING_RANGE=  0.700 !for crossing the Ewald sphere on shortest route
 REFLECTING_RANGE_E.S.D.=  0.092 !half-width (mosaicity) of REFLECTING_RANGE=

 SPACE_GROUP_NUMBER= 75   !0 for unknown crystals
 UNIT_CELL_CONSTANTS= 78.6   78.6   36.9   90.0  90.0  90.0
!Optional reindexing transformation to apply on reflection indices
!REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0

!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

!Generic file name, access, and format of data frames
 NAME_TEMPLATE_OF_DATA_FRAMES=../images/lys2_01???.img DIRECT RAXIS
 DATA_RANGE= 1  3      !Numbers of first and last data frame collected
 BACKGROUND_RANGE=1 3  !Numbers of first and last data frame for background
!Optional (0...10) frame ranges for looking for strong diffraction spots
 SPOT_RANGE=1  3       !First and last data frame number for finding spots

!This controls the parameters that are refined in "IDXREF" and "COLPROF".
!Refine AXIS if spots were picked from a large rotation range (>10 degrees).
 REFINE= ORIENTATION BEAM DISTANCE!AXIS

!Name of a reference data set
!REFERENCE_DATA_SET= CK.HKL

!>>>>>  Occasionally you want to modify the following parameters <<<<<<<<
 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 16000
 SPOT_WIDTH_ALONG_X=25       !Spot size (pixels) used by "INIT", "COLSPOT"
 SPOT_WIDTH_ALONG_Y=25       !Spot size (pixels) used by "INIT", "COLSPOT"
 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=8                !used by "COLSPOT"
 MINIMUM_SIGNAL_TO_NOISE_FOR_LOCATING_SPOTS= 5.0     !used by "COLSPOT"
 MINUTE=0   !Maximum number of minutes to wait until data frame must appears
 NUMBER_OF_REFLECTIONS_USED_FOR_REFINEMENT_IN_COLPROF=1000
 NUMBER_OF_FRAMES_BETWEEN_REFINEMENT_IN_COLPROF=-1  !-1:never refine;0:default
 WEAK= 6.0  !reflections with (I/sigma)<WEAK are weak (COLPROF, PROFIT)
 WFAC1=1.5  !This controls the number of rejected MISFITS in CORRECT;
	    !a larger value leads to fewer rejections.
 DELPHI= 5.0!controls the number of reference profiles and scaling factors
!File name, access, format of dark-current (non-Xray background) frame
!DARK_CURRENT_IMAGE=../images/blank.OSC DIRECT RAXIS

!>>>>>>>>>>> Additional parameters for fine tuning (rarely changed)
 MAXIMUM_RANDOM_DEVIATE_OF_INTENSITY=5.0  !Used in PROFIT
 RMAX=1.05        !Relative radius limiting trusted region on detector
 AIR=0.001        !Air absorption coefficient of x-rays
 INDEX_ERROR=0.05 INDEX_MAGNITUDE=8 INDEX_QUALITY=0.8!Used in IDXREF
 SEPMIN=6.0 CLUSTER_RADIUS=3                         !Used in IDXREF
 BFRAC=1.00       !rate for updating the background table  (COLPROF)
 MINPK=75   CUT=2.0
 TEST=1           !Test flag. 1,2 additional diagnostics and images
!used in CORRECT and GLOREF 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