!***************************************************************************** ! Example file XDS.INP for the ADSC Q315r CCD-detector ! At the NE-CAT beamline, sector 24ID-E at APS ! Characters in a line to the right of an exclamation mark are comment. !***************************************************************************** !NOTE: XDS can handle only "SMV" images of TYPE=unsigned_short. ! Images are expected to be already corrected for spatial distortions. ! ! !=============================================================== ! Values that need to be changed to reflect you experiment ! begin on line 156 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 ADSC Q315r that rarely need to be changed 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 ! if detector tilted, use !0.0 cos(2theta) sin(2theta) TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region ROTATION_AXIS= 1.0 0.0 0.0 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 !The following can be used to mask out the beamstop. !Generally this is not needed. Values for the masks can be obtained !by visually inspecting the images with a program such as ADXV. !UNTRUSTED_RECTANGLE= 570 1920 1469 2048 ! rectangle: X1 X2 Y1 Y2 !UNTRUSTED_ELLIPSE= 910 1110 1010 1210 ! ellipse enclosed by X1 X2 Y1 Y2 !UNTRUSTED_QUADRILATERAL=565 574 1519 1552 1508 1533 566 1536 !NX=number of fast pixels (along X); QX=length of a X-pixel (mm) !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm) !For the ADSC, the number of detector pixels and their sizes are !obtained from the image header. It is therefore unnecessary to !specify values for NX, NY, QX, QY. !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315r in binned mode !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r in unbinned mode !====================== 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)=!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. 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 !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 data images !Suggested values are listed near the end of INTEGRATE.LP !BEAM_DIVERGENCE= 0.200 !arctan(spot diameter/DETECTOR_DISTANCE) !BEAM_DIVERGENCE_E.S.D.= 0.020 !half-width (Sigma) of BEAM_DIVERGENCE !REFLECTING_RANGE= 0.500 !for crossing the Ewald sphere on shortest route !REFLECTING_RANGE_E.S.D.= 0.050 !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 !See XDSwiki for further explanation !of this parameter and how to use it !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 !====================== 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 = 0.10259 QY = 0.10259 !for ADSC Q315r in binned mode ! QX = 0.0513 QY = 0.0513 !for ADSC Q315r in unbinned more ! !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=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315r in binned mode !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r in unbinned mode ORGX=1536.0 ORGY=1536.8 !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_???.img !SMV 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