!*****************************************************************************
! 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 MAR CCD-detector at ESRF beamline ID14-1 *************
!********** and the 1024 X 1024 CCD-detector at CHESS            *************
!*****************************************************************************
!Standard settings for the MAR CCD that rarely need to be changed

 DETECTOR=CCDCHESS        MINIMUM_VALID_PIXEL_VALUE=0     OVERLOAD=65000
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
 RMAX=0.99        !Relative radius limiting trusted region on detector
!File name, access, format of dark-current (non-Xray background) image
!DARK_CURRENT_IMAGE=../images/blank.tif    !hardly ever used

 MAXIMUM_NUMBER_OF_PROCESSORS=2
 MINUTE=1   !Maximum number of minutes to wait until data image must appears
	    !MINUTE>0 implies that only one processor will be used
!TEST=1     !Test flag. 1,2 additional diagnostics and images

!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=2048 NY=2048 QX=0.079  QY=0.079   !MARCCD 165mm version
!NX=2048 NY=2048 QX=0.064  QY=0.064   !MARCCD 133mm version
!NX=1024 NY=1024 QX=0.0508 QY=0.0508  !CCD at CHESS
!
! Do not forget to define ORGX and ORGY, which are app. ORGX=NX/2, ORGY=NY/2

!====================== JOB CONTROL PARAMETERS ===============================
 JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
!JOB= INTEGRATE CORRECT
! JOB=XYCORR INIT COLSPOT IDXREF
!JOB=IDXREF DEFPIX
!JOB=XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN
!====================== GEOMETRICAL PARAMETERS ===============================

 ORGX=1035 ORGY=1044 !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
 DETECTOR_DISTANCE= 110.0   !(mm)

 ROTATION_AXIS= 1.0 0.0 0.0
 OSCILLATION_RANGE=0.5           !degrees (>0)

 X-RAY_WAVELENGTH=0.931       !Angstroem
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
 FRACTION_OF_POLARIZATION=0.95 !default=0.5 for unpolarized beam;0.90 at DESY;
 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
 AIR=0.001        !Air absorption coefficient of x-rays


!======================= CRYSTAL PARAMETERS =================================
 SPACE_GROUP_NUMBER=16   !0 for unknown crystals; cell constants are ignored.
 UNIT_CELL_CONSTANTS= 51.17   67.02   124.  90 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


!==================== 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.

!FRIEDEL'S_LAW=FALSE !Default is TRUE.

!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)


!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name, access, and format of data images
 NAME_TEMPLATE_OF_DATA_FRAMES=../datadir/trypsin_2_???.mccd DIRECT  TIFF

 DATA_RANGE=1  200

 BACKGROUND_RANGE=1 5

 SPOT_RANGE=1  40

 PROFILE_RANGE=1  10    !Up to 10 PROFILE_RANGE= parameters can be specified
 PROFILE_RANGE=40 50
 
 PROFILE_RANGE=101  110    !Up to 10 PROFILE_RANGE= parameters can be specified
  PROFILE_RANGE=140 150

!====================== 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


!================== 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=20.0 1.3 !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

!WFAC1=1.5  !This controls the number of rejected MISFITS in CORRECT;
	    !a larger value leads to fewer rejections.


!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!Parameters that are refined during the "INTEGRATE" step.
!Refinement is turned off if none of the keywords is specified.
 REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL !AXIS

!Specification of the peak profile parameters below overrides the automatic
!determination from the images specified in PROFILE_RANGE=
!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=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 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