Bruker data

Revision as of 18:02, 30 January 2012 by Kay (talk | contribs)

XDS wants "unwarped" Bruker frames. Unwarping can be done within Proteum2.


!*****************************************************************************
! Example file XDS.INP for Platinum135 CCD detector
! QX and QY are guesses only
!*****************************************************************************

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

 DATA_RANGE=1 60    !Numbers of first and last data image collected

 DETECTOR=SMARTCCD        MINIMUM_VALID_PIXEL_VALUE=1     OVERLOAD=1000000
 TRUSTED_REGION=0.0 1.5 !Relative radii limiting trusted detector region
!UNTRUSTED_ELLIPSE=1184 1289    1218 1322 ! ellipse   enclosed by X1 X2 Y1 Y2
!UNTRUSTED_RECTANGLE= 487  495     0 2528 ! rectangle enclosed by X1 X2 Y1 Y2
!UNTRUSTED_QUADRILATERAL=565 574  1519 1552  1508 1533  566 1536

!File name, access, and format of brass plate image
! BRASS_PLATE_IMAGE= ../images/spatial50_Still.sfrm  BRUKER DIRECT
!HOLE_DISTANCE=2.54   MXHOLE=1369     MNHOLE=800

!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 an X-pixel (mm)
!NY=number of slow pixels (along Y); QY=length of a  Y-pixel (mm)
!NX=1024 NY=1024 QX=0.089  QY=0.089  !Bruker SMART6000 CCD-detector
!NX=2048 NY=2048 QX=0.1785 QY=0.1785 !Bruker SMART CCD-detector
 NX=1024 NY=1024     !Bruker SMART6000 CCD-detector
! QX=0.0731 QY=0.0731 ! special to bypass problems with spatial corrections
QX=0.08984375 QY=0.08984375 ! may be correct
!====================== GEOMETRICAL PARAMETERS ===============================
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
 ORGX= 526  ORGY= 550   !Detector origin (pixels).
 DETECTOR_DISTANCE=  50.0   !(mm)

!DIRECTION_OF_DETECTOR_X-AXIS=cos(2theta),0,sin(2theta)
 DIRECTION_OF_DETECTOR_X-AXIS= 1.000000  0.000000  0.000000
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.000000  1.000000  0.000000

ROTATION_AXIS= 0.0 1.0 0.0       !SMARTCCD detector at BASF Ludwigshafen
!ROTATION_AXIS= 0.0 -1.0 0.0      !SMART6000 at Goettingen
!ROTATION_AXIS= -0.8165  -0.5773 0.0     !-sin(kappa) -cos(kappa)*cos(omega) sin(
omega)
!ROTATION_AXIS=  -0.58  -0.81 0.0 
!ROTATION_AXIS=  -0.552453 -0.833405 0
 OSCILLATION_RANGE=1.0            !degrees (>0)

 X-RAY_WAVELENGTH=1.54184         !Angstroem
 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 ! from xstal to detector
!FRACTION_OF_POLARIZATION=0.95 !default=0.5 for unpolarized beam;0.90 at DESY;
 POLARIZATION_PLANE_NORMAL= 1.0 0.0 0.0
!AIR=0.001    !Air absorption coefficient of x-rays as computed by XDS

!======================= CRYSTAL PARAMETERS =================================
 SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored.
 UNIT_CELL_CONSTANTS= 79.0  79.0  79.0    90.0 90.0 90.0

! 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= -1  0 -1  0 -1 -1  0  0  0  1  1  0

!FRIEDEL'S_LAW=FALSE !Default is TRUE.

!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=images/lysozyme_minute_01_????.sfrm  ! BRUKER

! BACKGROUND_RANGE=1 6  !Numbers of first and last data image for background

!SPOT_RANGE=  1 10     !First and last data image number for finding spots
!SPOT_RANGE=201 300
!SPOT_RANGE=401 500

!==================== 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=177.0      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

!====================== 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)=    AXIS  ! DISTANCE CELL ORIENTATION BEAM
!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=50.0 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=0.05 !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 images
!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 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