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9,159 bytes removed ,  18:24, 28 July 2019
Replaced content with "CCD detectors: XDS only reads "unwarped" Bruker "sfrm" format frames; unwarping can be done within the Bruker software called Proteum2. See also ccp4com:Bruker_data|Bruk..."
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XDS wants "unwarped" Bruker frames. Unwarping can be done within Proteum2.
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CCD detectors: XDS only reads "unwarped" Bruker "sfrm" format frames; unwarping can be done within the Bruker software called Proteum2. See also [[ccp4com:Bruker_data|Bruker data]].
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PHOTON detectors: XDS natively reads their .cbf files, and [[generate_XDS.INP]] generates XDS.INP for PHOTON II.
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<pre>
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Tim Grüne provides a program <code>sfrmtools</code> at [https://homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/] that extracts parameters relevant for data processing with XDS from headers of .sfrm files. See [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;ce43e97e.1907] .
!*****************************************************************************
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! Example file XDS.INP for Platinum135 CCD detector
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! QX and QY are guesses only
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!*****************************************************************************
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!====================== JOB CONTROL PARAMETERS ===============================
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!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
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JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
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DATA_RANGE=1 60    !Numbers of first and last data image collected
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DETECTOR=SMARTCCD        MINIMUM_VALID_PIXEL_VALUE=1    OVERLOAD=1000000
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TRUSTED_REGION=0.0 1.5 !Relative radii limiting trusted detector region
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!UNTRUSTED_ELLIPSE=1184 1289    1218 1322 ! ellipse  enclosed by X1 X2 Y1 Y2
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!UNTRUSTED_RECTANGLE= 487  495    0 2528 ! rectangle enclosed by X1 X2 Y1 Y2
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!UNTRUSTED_QUADRILATERAL=565 574  1519 1552  1508 1533  566 1536
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!File name, access, and format of brass plate image
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! BRASS_PLATE_IMAGE= ../images/spatial50_Still.sfrm  BRUKER DIRECT
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!HOLE_DISTANCE=2.54  MXHOLE=1369    MNHOLE=800
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!MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster
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!MAXIMUM_NUMBER_OF_PROCESSORS= 4!<33;ignored by single cpu version of xds
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!SECONDS=0  !Maximum number of seconds to wait until data image must appear
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!TEST=1    !Test flag. 1,2 additional diagnostics and images
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!NX=number of fast pixels (along X); QX=length of an X-pixel (mm)
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!NY=number of slow pixels (along Y); QY=length of a  Y-pixel (mm)
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!NX=1024 NY=1024 QX=0.089  QY=0.089  !Bruker SMART6000 CCD-detector
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!NX=2048 NY=2048 QX=0.1785 QY=0.1785 !Bruker SMART CCD-detector
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NX=1024 NY=1024    !Bruker SMART6000 CCD-detector
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! QX=0.0731 QY=0.0731 ! special to bypass problems with spatial corrections
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QX=0.08984375 QY=0.08984375 ! may be correct
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!====================== GEOMETRICAL PARAMETERS ===============================
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!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
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ORGX= 526  ORGY= 550  !Detector origin (pixels).
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DETECTOR_DISTANCE=  50.0  !(mm)
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!DIRECTION_OF_DETECTOR_X-AXIS=cos(2theta),0,sin(2theta)
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DIRECTION_OF_DETECTOR_X-AXIS= 1.000000  0.000000  0.000000
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DIRECTION_OF_DETECTOR_Y-AXIS= 0.000000  1.000000  0.000000
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ROTATION_AXIS= 0.0 1.0 0.0      !SMARTCCD detector at BASF Ludwigshafen
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!ROTATION_AXIS= 0.0 -1.0 0.0      !SMART6000 at Goettingen
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!ROTATION_AXIS= -0.8165  -0.5773 0.0    !-sin(kappa) -cos(kappa)*cos(omega) sin(
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omega)
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!ROTATION_AXIS=  -0.58  -0.81 0.0
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!ROTATION_AXIS=  -0.552453 -0.833405 0
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OSCILLATION_RANGE=1.0            !degrees (>0)
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X-RAY_WAVELENGTH=1.54184        !Angstroem
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INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 ! from xstal to detector
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!FRACTION_OF_POLARIZATION=0.95 !default=0.5 for unpolarized beam;0.90 at DESY;
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POLARIZATION_PLANE_NORMAL= 1.0 0.0 0.0
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!AIR=0.001    !Air absorption coefficient of x-rays as computed by XDS
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!======================= CRYSTAL PARAMETERS =================================
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SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored.
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UNIT_CELL_CONSTANTS= 79.0  79.0  79.0    90.0 90.0 90.0
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! You may specify here the x,y,z components for the unit cell vectors if
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! known from a previous run using the same crystal in the same orientation
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!UNIT_CELL_A-AXIS=
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!UNIT_CELL_B-AXIS=
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!UNIT_CELL_C-AXIS=
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!Optional reindexing transformation to apply on reflection indices
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!REIDX= -1  0 -1  0 -1 -1  0  0  0  1  1  0
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!FRIEDEL'S_LAW=FALSE !Default is TRUE.
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!REFERENCE_DATA_SET= CK.HKL  !Name of a reference data set (optional)
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!==================== SELECTION OF DATA IMAGES ==============================
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!Generic file name, access, and format of data images
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NAME_TEMPLATE_OF_DATA_FRAMES=images/lysozyme_minute_01_????.sfrm ! BRUKER
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! BACKGROUND_RANGE=1 6  !Numbers of first and last data image for background
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!SPOT_RANGE=  1 10    !First and last data image number for finding spots
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!SPOT_RANGE=201 300
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!SPOT_RANGE=401 500
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!==================== DATA COLLECTION STRATEGY (XPLAN) ======================
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!                      !!! Warning !!!
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! If you processed your data for a crystal with unknown cell constants and
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! space group symmetry, XPLAN will report the results for space group P1.
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!STARTING_ANGLE=177.0      STARTING_FRAME=1
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!used to define the angular origin about the rotation axis.
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!Default: STARTING_ANGLE=  0 at STARTING_FRAME=first data image
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!RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2
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!STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10
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!TOTAL_SPINDLE_ROTATION_RANGES=30.0 120 15
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!====================== INDEXING PARAMETERS =================================
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!Never forget to check this, since the default 0 0 0 is almost always correct!
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!INDEX_ORIGIN= 0 0 0          ! used by "IDXREF" to add an index offset
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!Additional parameters for fine tuning that rarely need to be changed
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!INDEX_ERROR=0.05 INDEX_MAGNITUDE=8 INDEX_QUALITY=0.8
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!SEPMIN=6.0 CLUSTER_RADIUS=3
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!MAXIMUM_ERROR_OF_SPOT_POSITION=3.0
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!MAXIMUM_ERROR_OF_SPINDLE_POSITION=2.0
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!MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.5
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!============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY =============
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!Decision constants for detection of lattice symmetry (IDXREF, CORRECT)
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MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated
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MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated
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!Decision constants for detection of space group symmetry (CORRECT).
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!Resolution range for accepting reflections for space group determination in
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!the CORRECT step. It should cover a sufficient number of strong reflections.
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TEST_RESOLUTION_RANGE=8.0 4.5
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MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas
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MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas
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!================= PARAMETERS CONTROLLING REFINEMENTS =======================
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!REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !DISTANCE
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REFINE(INTEGRATE)=    AXIS  ! DISTANCE CELL ORIENTATION BEAM
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!REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS
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!================== CRITERIA FOR ACCEPTING REFLECTIONS ======================
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VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX
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  !for excluding shaded parts of the detector.
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INCLUDE_RESOLUTION_RANGE=50.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT
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!used by CORRECT to exclude ice-reflections
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!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
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!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
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!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom
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!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom
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!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom
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!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong
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!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak
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!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong
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!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
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!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak
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!MINIMUM_ZETA=0.05 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT)
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!WFAC1=1.0  !This controls the number of rejected MISFITS in CORRECT;
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    !a larger value leads to fewer rejections.
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!REJECT_ALIEN=20.0 ! Automatic rejection of very strong reflections
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!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
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!Specification of the peak profile parameters below overrides the automatic
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!determination from the images
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!Suggested values are listed near the end of INTEGRATE.LP
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!BEAM_DIVERGENCE=  0.80  !arctan(spot diameter/DETECTOR_DISTANCE)
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!BEAM_DIVERGENCE_E.S.D.=  0.080 !half-width (Sigma) of BEAM_DIVERGENCE
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!REFLECTING_RANGE=  0.780 !for crossing the Ewald sphere on shortest route
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!REFLECTING_RANGE_E.S.D.=  0.113 !half-width (mosaicity) of REFLECTING_RANGE
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!NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=9 !used by: INTEGRATE
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!NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9    !used by: INTEGRATE
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!CUT=2.0    !defines the integration region for profile fitting
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!MINPK=75.0 !minimum required percentage of observed reflection intensity
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!DELPHI= 5.0!controls the number of reference profiles and scaling factors
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!======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) =======
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!MINIMUM_I/SIGMA=3.0 !minimum intensity/sigma required for scaling reflections
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!NBATCH=-1  !controls the number of correction factors along image numbers
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!REFLECTIONS/CORRECTION_FACTOR=50  !minimum #reflections/correction needed
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!PATCH_SHUTTER_PROBLEM=TRUE        !FALSE is default
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!STRICT_ABSORPTION_CORRECTION=TRUE  !FALSE is default
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!CORRECTIONS= DECAY MODULATION ABSORPTION
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!=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS =================
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!STRONG_PIXEL=3.0                              !used by: COLSPOT
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!A 'strong' pixel to be included in a spot must exceed the background
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!by more than the given multiple of standard deviations.
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!MAXIMUM_NUMBER_OF_STRONG_PIXELS=1500000      !used by: COLSPOT
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!SPOT_MAXIMUM-CENTROID=3.0                    !used by: COLSPOT
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!MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6          !used by: COLSPOT
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!This allows to suppress spurious isolated pixels from entering the
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!spot list generated by "COLSPOT".
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!NBX=3  NBY=3  !Define a rectangle of size (2*NBX+1)*(2*NBY+1)
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!The variation of counts within the rectangle centered at each image pixel
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!is used for distinguishing between background and spot pixels.
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!BACKGROUND_PIXEL=6.0                          !used by: COLSPOT,INTEGRATE
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!An image pixel does not belong to the background region if the local
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!pixel variation exceeds the expected variation by the given number of
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!standard deviations.
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!SIGNAL_PIXEL=3.0                              !used by: INTEGRATE
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!A pixel above the threshold contributes to the spot centroid
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</pre>
 
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