Bruker data: Difference between revisions

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


== SFRM files ==


<pre>
Bruker instruments save frames in SFRM file format.
!*****************************************************************************
XDS correctly reads these files. Data from CCD detectors, however, need to be "unwarped"; unwarping can be done within the Bruker software called Proteum2. See also [[ccp4com:Bruker_software|Bruker software]]. Data from more recent detectors, in particular all Photon detectors, do not need to unwarped and can be processed directly with XDS.
! Example file XDS.INP for Platinum135 CCD detector
! QX and QY are guesses only
!*****************************************************************************


!====================== JOB CONTROL PARAMETERS ===============================
For such files, [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;ce43e97e.1907 Tim Grüne] provides the program <code>sfrmtools</code> at [https://homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/]. It extracts parameters relevant for data processing with XDS from the header. The output should be saved in a file - only three more keyword/parameter lines are required for a minimal XDS.INP, namely e.g.
!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
NAME_TEMPLATE_OF_DATA_FRAMES=/my/data/name_????.sfrm
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
OVERLOAD=1000000
INCIDENT_BEAM_DIRECTION=0 0 1
Additional ones can of course be used to modify the operation of XDS, e.g.
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
INCLUDE_RESOLUTION_RANGE=50 1
TRUSTED_REGION=0 1.4142
! UNTRUSTED_QUADRILATERAL= <8 numbers, easily specified using XDSGUI>
...


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


DETECTOR=SMARTCCD        MINIMUM_VALID_PIXEL_VALUE=1    OVERLOAD=1000000
== CBF files ==
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
New detector types (optionally?) write CBF files, which XDS natively reads. [[generate_XDS.INP]] generates XDS.INP for CBF data written by the PHOTON II detector.
! 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>

Latest revision as of 09:53, 29 January 2020

SFRM files

Bruker instruments save frames in SFRM file format. XDS correctly reads these files. Data from CCD detectors, however, need to be "unwarped"; unwarping can be done within the Bruker software called Proteum2. See also Bruker software. Data from more recent detectors, in particular all Photon detectors, do not need to unwarped and can be processed directly with XDS.

For such files, Tim Grüne provides the program sfrmtools at [1]. It extracts parameters relevant for data processing with XDS from the header. The output should be saved in a file - only three more keyword/parameter lines are required for a minimal XDS.INP, namely e.g. 

NAME_TEMPLATE_OF_DATA_FRAMES=/my/data/name_????.sfrm
OVERLOAD=1000000 
INCIDENT_BEAM_DIRECTION=0 0 1

Additional ones can of course be used to modify the operation of XDS, e.g. 

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
INCLUDE_RESOLUTION_RANGE=50 1
TRUSTED_REGION=0 1.4142
! UNTRUSTED_QUADRILATERAL= <8 numbers, easily specified using XDSGUI>
...


CBF files

New detector types (optionally?) write CBF files, which XDS natively reads. generate_XDS.INP generates XDS.INP for CBF data written by the PHOTON II detector.

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