XDS.INP for Pohang Accelator Laboratory 7A

최근에 포항방사광가속기 beamline 7A에서 데이터 컬렉션을 해왔음. 포항에서 데이터 컬렉션을 한것은 처음인데, 비록 규모는 APS나 Spring-8과 같은 공룡빔라인에 비해서 작지만 비교적 잘 관리되고 업데이트된 곳이라고 생각함.

근데 대개의 빔라인이 그렇듯이 Data Reduction은 HKL2000를 사용하고 있고 HKL2000용 Site.def는 제공되고 있음. 그렇다면 열라비싼 상용프로그램인 HKL2000을 사용하지 않는 사람은 사이트에서 Data Reduction 해가야 되겠네? 이런 경우에는 무료로 제공되는 XDS를 이용하면 편함. 그러나 이건 GUI가 그닥 제대로 되어있지 않지? ㅋㅋㅋ 이런 것을 위해서 한번 XDS.INP를 만들어 보았음.

참고로 여기서 사용하는 Detector는 ADSC의 Q270. 기존의 ADSC용 XDS.INP를 조금 고치면 됨.

DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region

MAXIMUM_NUMBER_OF_JOBS=2  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster
MAXIMUM_NUMBER_OF_PROCESSORS=2!0)

X-RAY_WAVELENGTH=0.979          !Angstroem
INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
FRACTION_OF_POLARIZATION=0.90 !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
SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored.
UNIT_CELL_CONSTANTS= 59.57  69.69  56.97        90  90 90

!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)

INCLUDE_RESOLUTION_RANGE= 40.0 2.0
!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name, access, and format of data images
 NAME_TEMPLATE_OF_DATA_FRAMES=../crystal1_1_1_???.img  SMV DIRECT
 DATA_RANGE=1  360      !Numbers of first and last data image collected
 BACKGROUND_RANGE=1 6  !Numbers of first and last data image for background

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

!WFAC1=1.0  !This controls the number of rejected MISFITS in CORRECT;
        !a larger value leads to fewer rejections.


!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!Specification of the peak profile parameters below overrides the automatic
!determination from the data images
!Suggested values are listed near the end of INTEGRATE.LP
!BEAM_DIVERGENCE=  0.473  !arctan(spot diameter/DETECTOR_DISTANCE)
!BEAM_DIVERGENCE_E.S.D.=   0.047 !half-width (Sigma) of BEAM_DIVERGENCE
!REFLECTING_RANGE=  1.100 !for crossing the Ewald sphere on shortest route
!REFLECTING_RANGE_E.S.D.=  0.169 !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

!PATCH_SHUTTER_PROBLEM=TRUE         !FALSE is default
!STRICT_ABSORPTION_CORRECTION=FALSE !TRUE  is default


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


!================= PARAMETERS CONTROLLING REFINEMENTS =======================
!REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !DISTANCE
!REFINE(INTEGRATE)=!DISTANCE BEAM ORIENTATION CELL !AXIS
!REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS

사실 여기서 제일 중요한 게 다른것보다는 ORGX=2133.0 ORGY=2080.0 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
이걸 정하는건데 대충 NX, NY (이미지의 X Width, Y Height) 의 절반이라고 나와있지만 사실 빔센터가 항상 정확한게 아님. ㅋ

제일 좋은 방법은 빔센터를 직접 확인하는 것인데, adxv와 같은 뷰어로 img 파일을 불러보면
Screen Shot 2013-10-21 at 2.30.12 AM
요런식으로 빔센터의 X,Y Pixel 좌표를 찍어서 이것을 ORGX, ORGY로 잡으면 적절함.

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