!***************************************************************************** ! Example file XDS.INP for the PILATUS 6M pixel detector at ! NE-CAT sector 24ID-C at APS. ! Characters in a line to the right of an exclamation mark are comment. !***************************************************************************** !=============================================================== ! Values that need to be changed to reflect you experiment ! begin on line 168 of this file! ! search for "VALUES TO CHECK" ! ! ! The remaining lines contain standard settings that may need to changed ! for difficult to process data. ! ! Information on the XDS program package may be found at: ! http://http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html ! ! The XDSwiki can be found at: ! http://http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page !=============================================================== !Standard settings for the PILATUS 6M that rarely need to be changed DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=1048500 SENSOR_THICKNESS=0.32 !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=2463 NY=2527 QX=0.172 QY=0.172 !PILATUS 6M UNTRUSTED_RECTANGLE= 487 495 0 2527 ! these do not have to be specified UNTRUSTED_RECTANGLE= 981 989 0 2527 ! but it is better to do so UNTRUSTED_RECTANGLE=1475 1483 0 2527 ! UNTRUSTED_RECTANGLE=1969 1977 0 2527 ! Values have been painstakingly UNTRUSTED_RECTANGLE= 0 2463 195 213 ! checked by KD 2012-01-14 UNTRUSTED_RECTANGLE= 0 2463 407 425 ! UNTRUSTED_RECTANGLE= 0 2463 619 637 ! UNTRUSTED_RECTANGLE= 0 2463 831 849 ! UNTRUSTED_RECTANGLE= 0 2463 1043 1061 ! UNTRUSTED_RECTANGLE= 0 2463 1255 1273 ! UNTRUSTED_RECTANGLE= 0 2463 1467 1485 ! UNTRUSTED_RECTANGLE= 0 2463 1679 1697 ! UNTRUSTED_RECTANGLE= 0 2463 1891 1909 ! UNTRUSTED_RECTANGLE= 0 2463 2103 2121 ! UNTRUSTED_RECTANGLE= 0 2463 2315 2333 ! !The following can be used to mask the beamstop, but are normally unnecessary !If used, visually inspect your images to determine the appropriate parameters !UNTRUSTED_ELLIPSE=1184 1289 1218 1322 ! ellipse enclosed by X1 X2 Y1 Y2 !UNTRUSTED_QUADRILATERAL=565 574 1519 1552 1508 1533 566 1536 !MINIMUM_FRACTION_OF_BACKGROUND_REGION=0.01 !X-GEO_CORR=GD_6M_X06SA_SLS_27022007_X.pck CCP4 !Y-GEO_CORR=GD_6M_X06SA_SLS_27022007_Y.pck CCP4 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ! if detector titled use ! 0.0 cos(2theta) sin(2theta) ROTATION_AXIS= 1.0 0.0 0.0 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !====================== 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 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)=!DISTANCE BEAM ORIENTATION CELL !AXIS !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. !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=13!used by: INTEGRATE !NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9 !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, but read Tips and Tricks in XDSwiki !CORRECTIONS= DECAY MODULATION ABSORPTION !=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS ================= STRONG_PIXEL=6.0 !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 !DATA_RANGE_FIXED_SCALE_FACTOR= 1 60 1.0 ! used by : INIT,INTEGRATE !====================== VALUES TO CHECK FOR YOU EXPERIMENT =================== !====================== GEOMETRICAL PARAMETERS =============================== !ORGX and ORGY are the XDS beam center (in pixels) ! ORGX = <* HKL-2000 y beam divided by pixel size (QX) *> ! ORGY = <* HKl-2000 x beam divided by pixel size (QY) *> ! QX = 0.172 QY = 0.172 !for PILATUS 6M ! !If you do not know the precise beam center, ORGX and ORGY !are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 !NX=2463 NY=2527 QX=0.172 QY=0.172 !PILATUS 6M ORGX=1231.5 ORGY=1263.5 !Detector origin (pixels). DETECTOR_DISTANCE= 105.33 !(mm) OSCILLATION_RANGE=1.0 !degrees (>0) X-RAY_WAVELENGTH=0.980 !Angstroem INCLUDE_RESOLUTION_RANGE=200.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT !Change values to adjust resolution limits !of your data set. !======================= CRYSTAL PARAMETERS ================================= !SPACE_GROUP_NUMBER=168 !0 for unknown crystals; cell constants are ignored. ! UNIT_CELL_CONSTANTS= 90.396 90.396 45.466 90 90 120 !If space group and/or cell constants are not provided, XDS will calculate !them based on the diffraction pattern in the IDXREF and CORRECT steps. ! 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, which is appropriate for NATIVE data. !Use FALSE for anomalous data or when you want to keep !Friedel pairs separate during integration. !==================== SELECTION OF DATA IMAGES ============================== ! VERY IMPORTANT TO CHANGE THE FOLLOWING TO MATCH YOUR DATA ! !Generic file name and format (optional) of data images NAME_TEMPLATE_OF_DATA_FRAMES=../images/mb1_1_????.cbf !CBF DATA_RANGE=1 20 !Numbers of first and last data image collected BACKGROUND_RANGE=1 6 !Numbers of first and last data image for background !Used by INIT !SPOT_RANGE= is used by COLSPOT and IDXREF. If not specfied, entire data ! data range is used to pick peaks for indexing the data. SPOT_RANGE=1 5 !First and last data image number for finding spots !SPOT_RANGE=7 18 !First and last data image number for finding spots !SPOT_RANGE=20 20 !First and last data image number for finding spots !====================== JOB CONTROL PARAMETERS =============================== !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 !The above speeds up COLSPOT & INTEGRATE on multi processor computers !Change JOB= card to indicate which steps you want XDS to run. JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT!equal to JOB=ALL