!*****************************************************************************
! Example file XDS.INP for ADSC CCD detector at CHESS 
! Characters in a line to the right of an exclamation mark are comment.
!*****************************************************************************
!NOTE: XDS can handle only "SMV" images of TYPE=unsigned_short.
! Images are expected to be already background-subtracted and corrected for
!   spatial distortions.
!
!Standard settings for the detector that rarely need to be changed

 DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000
 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 1.05 !Relative radii limiting trusted detector region
!UNTRUSTED_RECTANGLE= 570 1920  1469 2048  ! rectangle: X1 X2   Y1 Y2  
!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)
!For the ADSC, the number of detector pixels and their sizes are
!obtained from the image header. It is therefore unnecessary to
!specify values for NX, NY, QX, QY.
!
! Detectors at CHESS
!
!NX=2048 NY=2048 QX=0.1024 QY=0.1024   !ADSC Q210 at A1 (binned)
!NX=4096 NY=4096 QX=0.0512 QY=0.0512   !ADSC Q210 at A1 (unbinned)
!
!NX=2084 NY=2084 QX=0.1296 QY=0.1296   !ADSC Q270 at F1 (binned)
!NX=4168 NY=4168 QX=0.0648 QY=0.0648   !ADSC Q270 at F1 (unbinned)
!
!NX=1152 NY=1152 QX=0.1632 QY=0.1632   !ADSC Q4 at F3 (binned, rarely used!!)
!NX=2304 NY=2304 QX=0.0816 QY=0.0816   !ADSC Q4 at F3 (unbinned)

!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).
ORGX=1064.0  ORGY=1104.0  
            ! Using (X/pixsize),(npix-(Y/pixsize)); X,Y from ADX mm coords,
            ! equivalent to (Y/pixsize),(X/pixsize); X,Y from denzo or mosflm

 DETECTOR_DISTANCE= 140.0  !(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=1.0            ! 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
! X-RAY_WAVELENGTH=1.7311         ! Angstroem, F3 varies, this is for Fe edge
! 

 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_???.img  !SMV

 DATA_RANGE=1  10      !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 =======================
!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=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=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