Re: [ccp4bb] xds undefined data range error

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: mtz2various is broken [ was: Another pointless question ]
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-06-11

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Subject: Re: xds undefined data range error
From: Sangeetha Vedula sangeetha {- dot -} bb {- at -} GMAIL {- dot -} COM
Date: 2009-06-11

Subject: Re: xds undefined data range error
From: Christopher Bahl ccp4 {- dot -} bahl {- at -} GMAIL {- dot -} COM
Date: 2009-06-11

!*****************************************************************************
! File XDS.INP containing named arguments for running XDS (arbitrary order).
! For further explanations of the meaning of these parameters see 'xds.man'.
! Characters in a line to the right of an exclamation mark are comment.
!*****************************************************************************
!*************** Example for MAR345 IP at Dartmouth Med School ***************
!*****************************************************************************
!

!====================== JOB CONTROL PARAMETERS ===============================
! JOB= XDS !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
JOB= DEFPIX INTEGRATE CORRECT

!====================== GEOMETRICAL PARAMETERS ===============================
DETECTOR_DISTANCE= 145 !(mm)
OSCILLATION_RANGE= 0.2 !degrees (>0)
ORGX=1045 ORGY=1047 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
!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

!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name, access, and format of data images
NAME_TEMPLATE_OF_DATA_FRAMES= ../ja001.uber/JA001_1_???.img SMV DIRECT

DATA_RANGE=1 900 !Numbers of first and last data image collected

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

SPOT_RANGE=1 900 !First and last data image number for finding spots
!SPOT_RANGE=64 68 !Up to 10 SPOT_RANGE= parameters can be specified
!SPOT_RANGE=220 230
!SPOT_RANGE=340 350

!======================= CRYSTAL PARAMETERS =================================
SPACE_GROUP_NUMBER= 5 !0 for unknown crystals; cell constants are ignored.
UNIT_CELL_CONSTANTS= 168.179 83.944 89.184 90 100.392 90

!Optional reindexing transformation to apply on reflection indices
!REIDX= 1 0 0 1 0 1 0 0 0 0 1 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=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= 50.0 1.55 !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=1.5 !This controls the number of rejected MISFITS in CORRECT;
!a larger value leads to fewer rejections.

!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!Parameters that are refined during the "INTEGRATE" step.
!Refinement is turned off if none of the keywords is specified.
REFINE(INTEGRATE)=! DISTANCE ORIENTATION AXIS CELL !BEAM

!Specification of the peak profile parameters below overrides the automatic
!determination from the images specified in PROFILE_RANGE=
!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

!=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS =================
STRONG_PIXEL= 4 !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= 20 !used by: COLSPOT
!This allows to suppress spurious isolated pixels from entering the
!spot list generated by "COLSPOT".

NBX=4 NBY=4 !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

!==================== BEAM CHARACTERISTICS ==================================
X-RAY_WAVELENGTH= 0.9782 !Angstroem
FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam;0.90 at DESY;
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0

!==================== DATA PROCESSING PARAMETERS ============================
MAXIMUM_NUMBER_OF_PROCESSORS=10!<25;ignored by single cpu version of xds

!==================== 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.

FRIEDEL'S_LAW=TRUE !Default is TRUE.

!RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2

STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 0 10 !180 10

TOTAL_SPINDLE_ROTATION_RANGES= 40 60 10

!REFERENCE_DATA_SET= CK.HKL !Name of a reference data set (optional)

!==================== DETECTOR IDENTITY/GEOMETRY ============================
DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000
NX=2084 NY=2084 QX=0.1296 QY=0.1296 !ADSC Q270 2x2bin IP
!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)
!
! Do not forget to define ORGX and ORGY, which are app. ORGX=NX/2, ORGY=NY/2

INCIDENT_BEAM_DIRECTION= 0 0 1
ROTATION_AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
AIR=0.001 !Air absorption coefficient of x-rays

!File name, access, format of dark-current (non-Xray background) image
!DARK_CURRENT_IMAGE=../images/blank.tif !hardly ever used

!MINUTE=0 !Maximum number of minutes to wait until data image must appears
!MINUTE>0 implies that only one processor will be used
!TEST=1 !Test flag. 1,2 additional diagnostics and images

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: mtz2various is broken [ was: Another pointless question ]
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-06-11

Next message:
Subject: Re: xds undefined data range error
From: Sangeetha Vedula sangeetha {- dot -} bb {- at -} GMAIL {- dot -} COM
Date: 2009-06-11