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CCP4BB  June 2009

CCP4BB June 2009

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Subject:

Re: xds undefined data_range error

From:

Christopher Bahl <[log in to unmask]>

Reply-To:

Christopher Bahl <[log in to unmask]>

Date:

Thu, 11 Jun 2009 11:45:52 -0400

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (75 lines) , XDS.INP (167 lines)

Hi Sangeetha,
Here is an XDS.INP that I recently used to process data from X6A; you 
could try inputing your parameters in this file (or at least compare the 
two).
Hope that helps, and good luck!
-Chris

-- 
Christopher Bahl
Dartmouth Biochemistry
7200 Vail Bldg.
Hanover, NH  03755
Phone: (603) 650-1174
Fax: (603) 650-1128


Sangeetha Vedula wrote:
> I checked:
>
> 1. I did name it XDS.INP; no problem there.
> 2. The path along with file name template is only about 30 characters.
> 3. No. of files = 156 (DATA_RANGE=1 156)
> 4. Edited Nx, Ny, Qx, Qy (unless the image header is wrong, which 
> could cause problems, but why does it have a problem with data range?).
>
> I am attaching the file, XDS.INP that I am using. Thank you so much in 
> advance for taking the time.
>
> Regards,
>
> Sangeetha.
>
> On Thu, Jun 11, 2009 at 3:23 AM, Kay Diederichs 
> <[log in to unmask] 
> <mailto:[log in to unmask]>> wrote:
>
>     Sangeetha Vedula schrieb:
>
>         Hello all,
>
>         Apologies for the non-CCP4 question.
>
>         I am trying to process some data collected at X6A in March. I
>         edited the XDS.inp file for ADSC detector. When I try to run
>         xds, however, it gives an error immediately:
>
>         !!! ERROR !!! UNDEFINED DATA_RANGE=
>
>         I checked the data range and the image path and template I
>         gave. Doesn't appear to be anything wrong. What could be
>         causing the error, though?
>
>         Thanks for any input and suggestions!
>
>         Sangeetha.
>
>
>     Hello Sangeetha,
>
>     please post your XDS.INP for us to check.
>
>     Kay
>     -- 
>     Kay Diederichs                
>     http://strucbio.biologie.uni-konstanz.de
>     email: [log in to unmask]
>     <mailto:[log in to unmask]>     Tel +49 7531 88 4049
>     Fax 3183
>     Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457
>     Konstanz
>
>




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

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