Bruker data: Difference between revisions

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(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.
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]].


PHOTON detectors: XDS natively reads their .cbf files, and [[generate_XDS.INP]] generates XDS.INP for PHOTON II.


<pre>
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] .
!*****************************************************************************
! 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
</pre>

Revision as of 19:24, 28 July 2019

CCD detectors: XDS only reads "unwarped" Bruker "sfrm" format frames; unwarping can be done within the Bruker software called Proteum2. See also Bruker data.

PHOTON detectors: XDS natively reads their .cbf files, and generate_XDS.INP generates XDS.INP for PHOTON II.

Tim Grüne provides a program sfrmtools at [1] that extracts parameters relevant for data processing with XDS from headers of .sfrm files. See [2] .

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