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crystallography:collection:frx_xds_input [2016/12/06 13:28] – bonnefoncrystallography:collection:frx_xds_input [2023/11/01 20:19] (current) – external edit 127.0.0.1
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-==== XDS.INP input file for data collected on Rigaku FR-X ====+==== XDS.INP input file for data collected on Rigaku FR-X with EIGER 4M ====
  
 <code> <code>
-!***************************************************************************** +!*********************************************************************************! 
-! Example file XDS.INP for the PILATUS 200K pixel detector from Rigaku. +! Example file XDS.INP for the EIGER 4M pixel detector, IGBMC CBI                 ! 
-! Characters in a line to the right of an exclamation mark are comment. +!                                                                                 !       
-!***************************************************************************** +! Last edit: Alastair McEwen, 2017/07/06                                          ! 
-!==== Often it is necessary to use  MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=1 +!*********************************************************************************! 
-!==== DETECTOR PARAMETERS ... PLEASE CHANGE DISTANCE and 2THETA and BEAM POSITION +
-!====================== GEOMETRICAL PARAMETERS ===============================+
  
-!BEAM POSITION on the detector in pixels is ORGX and ORGY +!============================ JOB CONTROL PARAMETERS =============================!
-!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 +
-ORGX= 207.68 ORGY= 307.84 !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2 +
- +
-!2theta 0 +
-DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0  +
-DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0  +
- +
-!2theta 2T +
-!DIRECTION_OF_DETECTOR_X-AXIS= 0.0 cos(2T) sin(2T) +
-!DIRECTION_OF_DETECTOR_Y-AXIS= 1.0  0.0 0.0 +
- +
-DETECTOR_DISTANCE= 50   !(mm) +
- +
-!Other detector stuff probably should be unchanged +
- +
-DETECTOR=PILATUS         MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=1048500 +
-SENSOR_THICKNESS=0.45        !SILICON=-1.0 +
-!AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default +
-!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=981 NY=1043 QX=0.172  QY=0.172  !PILATUS3 X CdTe 1M +
-NX=487 NY= 619 QX=0.172  QY=0.172  !PILATUS 300K +
-!NX=487 NY= 407 QX=0.172  QY=0.172  !PILATUS 200K +
-!UNTRUSTED_RECTANGLE= 487  495     0 2528 +
-!UNTRUSTED_RECTANGLE=   0 2464   195  213 +
-!UNTRUSTED_RECTANGLE=   0 2464   407  425 +
-UNTRUSTED_RECTANGLE= 0 488 195 213  +
-UNTRUSTED_RECTANGLE= 0 488 407 425 +
-!UNTRUSTED_QUADRILATERAL=565 574  1519 1552  1508 1533  566 1536 +
-!MINIMUM_FRACTION_OF_BACKGROUND_REGION=0.01 +
- +
-TRUSTED_REGION=0.0 1.41 !Relative radii limiting trusted detector region +
- +
-!MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster +
-!MAXIMUM_NUMBER_OF_PROCESSORS=8!<32;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 +
- +
-!=== CRYSTAL GONIOMETER which vector was the crystal rotated around? +
- +
-ROTATION_AXIS= 1.0 0.0 0.0 +
- +
-!====================== JOB CONTROL PARAMETERS =============================== +
-!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT+
 JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 +!JOB= INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 + MAXIMUM_NUMBER_OF_PROCESSORS=4
  
-!=== X-RAY SOURCE PROPERTIES =====  Probably will not change +!====================== GEOMETRICAL PARAMETERS ===================================! 
- + ORGX=1010.21  ORGY=831.47        !Detector origin (pixels) 
-X-RAY_WAVELENGTH=1.54187           !Angstroem + DETECTOR_DISTANCE= 61            !(mm) (range = 61 - 280) 
-INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 + OSCILLATION_RANGE=0.25           !degrees (>0) 
-FRACTION_OF_POLARIZATION=0.50 !default=0.5 for unpolarized beam + X-RAY_WAVELENGTH=1.54178         !Angstroem (do not change) 
-POLARIZATION_PLANE_NORMAL= 1.0 0.0 0.0 + STARTING_ANGLE=-68               !degrees
-!FRACTION_OF_POLARIZATION=0.99 !synchrotron, default=0.5 for unpolarized beam +
-!POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 ! synchrotron +
- +
-!==================== SELECTION OF DATA IMAGES ============================== +
-!Generic file name and format (optional) of data images +
- +
-NAME_TEMPLATE_OF_DATA_FRAMES=/directory/***.img +
-!Optimal choice is 0.5*mosaicity (REFLECTING_RANGE_E.S.D.= mosaicity) +
-OSCILLATION_RANGE=0.10            !degrees (>0) +
-STARTING_ANGLE=  -90.0       +
-STARTING_FRAME=1 +
-DATA_RANGE=1 1620       !Numbers of first and last data image collected +
- +
-!BACKGROUND_RANGE=1 6  !Numbers of first and last data image for background +
- +
-SPOT_RANGE=1 810       !First and last data image number for finding spots +
- +
-!======================= CRYSTAL PARAMETERS ================================= +
-SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored. +
-UNIT_CELL_CONSTANTS=    60 70 80 90 90 90 +
- +
-!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+!======================= CRYSTAL PARAMETERS ======================================! 
 + SPACE_GROUP_NUMBER=0   !0 for unknown crystals; cell constants are ignored. 
 + UNIT_CELL_CONSTANTS= 77.7 77.7 77.7 90 90 90
 !REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0 !REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0
 + FRIEDEL'S_LAW=FALSE !Default is TRUE
  
-FRIEDEL'S_LAW=FALSE !Default is TRUE.+!==================== SELECTION OF DATA IMAGES ===================================! 
 + NAME_TEMPLATE_OF_DATA_FRAMES=path-to/Image_????.img 
 + STARTING_FRAME=101      !Number of first image 
 + DATA_RANGE=1 720        !Numbers of first and last data image collected 
 +!BACKGROUND_RANGE=1  40  !rather use defaults (first 5 degrees of rotation) 
 + SPOT_RANGE=1 360        !First and last data image number for finding spots 
 +!REFERENCE_DATA_SET=./XDS_ASCII.HKL
  
-!REFERENCE_DATA_SET= CK.HKL   !Name of a reference data set (optional) +!================= PARAMETERS CONTROLLING REFINEMENTS ============================! 
-!FIT_B-FACTOR_TO_REFERENCE_DATA_SET=TRUE ! default is FALSE+ REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS !DISTANCE POSITION 
 + REFINE(INTEGRATE)=DISTANCE POSITION BEAM ORIENTATION ! AXIS CELL 
 +!REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS DISTANCE POSITION !Default is: refine everything
  
-!==================== DATA COLLECTION STRATEGY (XPLAN) ====================== +!======================== DETECTOR AND GENERATOR PARAMETERS ======================! 
-!                       !!! Warning !!! + DETECTOR=EIGER          
-!If you processed your data for a crystal with unknown cell constants and + MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=2147483647 
-!space group symmetry, XPLAN will report the results for space group P1.+ SENSOR_THICKNESS=0.45     
 + NX=2070 NY=2167 QX=0.075 QY=0.075 
 + DIRECTION_OF_DETECTOR_X-AXIS=0.927184 0 0.374607 !cos(2theta) 0 sin(2theta) 
 + DIRECTION_OF_DETECTOR_Y-AXIS=0.0 1.0 0.0 
 + ROTATION_AXIS=0 -1 0 
 + INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 
 + POLARIZATION_PLANE_NORMAL=1 0 0 
 + FRACTION_OF_POLARIZATION=0.50 !default=0.5 for unpolarized beam 
 + TRUSTED_REGION=0.0 1.2 ! partially use corners of detector (0 1.4143: use all pixels) 
 +  
 + UNTRUSTED_RECTANGLE= 1030 1041    0 2168 
 + UNTRUSTED_RECTANGLE=    0 2071  514  552 
 + UNTRUSTED_RECTANGLE=    0 2071 1065 1103 
 + UNTRUSTED_RECTANGLE=    0 2071 1616 1654
  
-!STARTING_ANGLE=  0.0      STARTING_FRAME=1 +!====================== INDEXING PARAMETERS ======================================! 
-!used to define the angular origin about the rotation axis. + STRONG_PIXEL=4           ! COLSPOT: only use strong reflections (default is 3) 
-!Default:  STARTING_ANGLE=  0 at STARTING_FRAME=first data image+ MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
  
-!RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2 +!============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY ==================!
- +
-!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=4.0       ! default is 6 for other detectors +
-CLUSTER_RADIUS=2 ! default is 3 for other detectors +
-!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) !Decision constants for detection of lattice symmetry (IDXREF, CORRECT)
-MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated  + MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated  
-MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated+ MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated
  
 !Decision constants for detection of space group symmetry (CORRECT).  !Decision constants for detection of space group symmetry (CORRECT). 
 !Resolution range for accepting reflections for space group determination in !Resolution range for accepting reflections for space group determination in
 !the CORRECT step. It should cover a sufficient number of strong reflections. !the CORRECT step. It should cover a sufficient number of strong reflections.
-TEST_RESOLUTION_RANGE=8.0 4.5  + TEST_RESOLUTION_RANGE=8.0 4.5  
-MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas + MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas 
-MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas + MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas
-  +
-!================= PARAMETERS CONTROLLING REFINEMENTS ======================= +
-!REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !POSITION +
-!REFINE(INTEGRATE)=!POSITION BEAM ORIENTATION CELL !AXIS +
-!REFINE(CORRECT)=POSITION BEAM ORIENTATION CELL AXIS+
  
-!================== CRITERIA FOR ACCEPTING REFLECTIONS ====================== +!================== CRITERIA FOR ACCEPTING REFLECTIONS ===========================! 
-VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX+ VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000. 30000. !Used by DEFPIX
     !for excluding shaded parts of the detector.     !for excluding shaded parts of the detector.
  
-INCLUDE_RESOLUTION_RANGE=50.0 0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT+ INCLUDE_RESOLUTION_RANGE=50.0 1.5 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT
  
 !used by CORRECT to exclude ice-reflections !used by CORRECT to exclude ice-reflections
Line 159: Line 90:
 !EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak !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 !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 ===================== !============== 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=13 !used by: INTEGRATE+ NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13!used by: INTEGRATE
 !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9     !used by: INTEGRATE !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9     !used by: INTEGRATE
 +</code>
  
-!DELPHI= 6.0!controls the number of reference profiles and scaling factors +{{ :crystallography:collection:cbi-eiger-4m-xds-v1.inp |}}
-!CUT=2.0    !defines the integration region for profile fitting +
-!MINPK=75.0 !minimum required percentage of observed reflection intensity+
  
-!======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) ======= +{{ :crystallography:collection:pilatus300k_frx_xds.inp |}}
-!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=1!3        !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 +
- +
-!DATA_RANGE_FIXED_SCALE_FACTOR= 1 60 1.0 ! used by : INIT,INTEGRATE +
-</code>+
crystallography/collection/frx_xds_input.1481030894.txt.gz · Last modified: (external edit)