EIGER-XDS.INP

!*****************************************************************************

! LS-CAT 21-D

! XDS.INP template for ! EIGER 9M with 0.45 mm thick silicon sensors.

! NOTE: XDS will work pending that H5ToXDS is on your PATH

! Characters to the right of an exclamation mark are comments.

! This file was autogenerated by XDS_from_H5.py (Oct 2015).

! Please check default values before processing.

! For questions and comments please contact docandreas@gmail.com.

!*****************************************************************************

!============== DETECTOR PARAMETERS =============================

DETECTOR=EIGER

MINIMUM_VALID_PIXEL_VALUE=0

OVERLOAD= 1074913 ! taken from HDF5 header item

! /entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff

SENSOR_THICKNESS=0.45 ! [mm]

QX=0.075 QY=0.075 ! [mm]

NX= 3110 NY= 3269

!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 9M DETECTOR

UNTRUSTED_RECTANGLE= 1030 1041 0 3270

UNTRUSTED_RECTANGLE= 2070 2081 0 3270

!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER 9M DETECTOR

UNTRUSTED_RECTANGLE= 0 3111 514 552

UNTRUSTED_RECTANGLE= 0 3111 1065 1103

UNTRUSTED_RECTANGLE= 0 3111 1616 1654

UNTRUSTED_RECTANGLE= 0 3111 2167 2205

UNTRUSTED_RECTANGLE= 0 3111 2718 2756

TRUSTED_REGION=0.0 1.41 !Relative radii limiting trusted detector region

DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0

DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ! 0.0 cos(2theta) sin(2theta)

!====================== JOB CONTROL PARAMETERS ========================

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT

! JOB= INTEGRATE CORRECT

MAXIMUM_NUMBER_OF_JOBS=8 !Speeds up COLSPOT & INTEGRATE on multicore machine

MAXIMUM_NUMBER_OF_PROCESSORS=4!<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

!====================== GEOMETRICAL PARAMETERS =======================

!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2

ORGX= 1547.0 ORGY= 1634.0 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2

! CHANGE BASED ON YOUR EXP

DETECTOR_DISTANCE= 100 ! [mm]

ROTATION_AXIS= 1.0 0.0 0.0

! Optimal choice is 0.5*mosaicity (REFLECTING_RANGE_E.S.D.= mosaicity)

! CHANGE BASED ON YOUR EXP

OSCILLATION_RANGE=0.50000 ! [deg] (>0)

!CHANGE BASED ON YOUR EXP

X-RAY_WAVELENGTH=1.2398 ! [A]

INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0

FRACTION_OF_POLARIZATION=0.99 !default=0.5 for unpolarized beam

POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0

!======================= CRYSTAL PARAMETERS ===========================

SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored.

UNIT_CELL_CONSTANTS= 78.4452 78.4452 78.4452 90.000 90.000 90.000

! 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= 0 0 -1 0 0 -1 0 0 -1 0 0 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 and format (optional) of data images

! CHANGE BASED ON YOUR EXP, THIS IS THE MASTER FILE

NAME_TEMPLATE_OF_DATA_FRAMES=../h.001_??????.h5 ! HDF5

! CHANGE BASED ON YOUR EXP

DATA_RANGE=1 200

BACKGROUND_RANGE=1 20 ! Numbers of first and last data image for background

!Five degrees are sufficient

SPOT_RANGE= 1 100 ! First image range for finding spots

! SPOT_RANGE= 361 381 ! Second image range for finding spots

! SPOT_RANGE= 700 720 ! Third image range for finding spots

!Use all images if three ranges are not sufficient

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

!====================== 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)

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 3

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 ! POSITION

REFINE(IDXREF)= DISTANCE BEAM ORIENTATION CELL AXIS

! REFINE(INTEGRATE)= POSITION ORIENTATION ! BEAM CELL AXIS

REFINE(INTEGRATE)= DISTANCE POSITION ORIENTATION BEAM CELL AXIS

! REFINE(CORRECT)= POSITION BEAM ORIENTATION CELL AXIS

REFINE(CORRECT)= DISTANCE POSITION 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 !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=21!used by: INTEGRATE

NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=21 !used by: INTEGRATE

!DELPHI= 6.0!controls the number of reference profiles and scaling factors

!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) =====

!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=4.0 !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=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

!FIXED_SCALE_FACTOR=TRUE !Default is FALSE; used by : INIT,INTEGRATE