Donghui,
there are several ways to get ORGX ORGY parameters. As Juergen suggested,
you could use the numbers from the header or Mosflm output.
More information on the excellent XDS Wiki:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Obtaining_ORGX_ORGY
Another option would be to run generate_XDS.INP script, which will get
ORGX ORGY parameters from headers automatically:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
If you know the spacegroup, define it with keyword SPACE_GROUP_NUMBER=
(your script has 0).
HTH,
Konstantin
On Wed, 8 Dec 2010, wu donghui wrote:
> Dear all,
> Recently I collected several data sets at 13B1 Taiwan beamline with Q315r
> detector. It's no problem to index these datasets using mosflm, but Rms
> residual and weighted residual is high. Here I want to try XDS to play my
> data. I downloaded a template example as below.
>
> !************************************************************************
> *****
> ! Example file XDS.INP for the ADSC Q105 CCD-detector
> ! 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.
> !
> !Standard settings for the ADSC Q105 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
> TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region
> !UNTRUSTED_RECTANGLE= 570 1920 1469 2048 ! rectangle: X1 X2 Y1 Y2
> !UNTRUSTED_ELLIPSE= 910 1110 1010 1210 ! ellipse enclosed by X1 X2 Y1
> Y2
> !File name, access, format of dark-current (non-Xray background) image
> !DARK_CURRENT_IMAGE=../images/blank.tif !hardly ever used
>
> !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
> !MINUTE=0 !Maximum number of minutes to wait until data image must
> appears
> !TEST=1 !Test flag. 1,2 additional diagnostics and images
>
> !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=2304 NY=2304 QX=0.0816 QY=0.0816 !ADSC Q4
> !NX=2048 NY=2048 QX=0.0500 QY=0.0500 !ADSC Q105
> !NX=2048 NY=2048 QX=0.1024 QY=0.1024 !ADSC Q210 at ESRF ID-29
> !NX=4096 NY=4096 QX=0.051 QY=0.051 !ADSC Q210r
> !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2
> !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r at ESRF ID-29
>
> !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by
> default
>
> !====================== JOB CONTROL PARAMETERS
> ===============================
> !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
>
> !====================== GEOMETRICAL PARAMETERS
> ===============================
> !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2,
> ORGY=NY/2
> ORGX=3072.0 ORGY=3072 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
> DETECTOR_DISTANCE= 480 !(mm)
>
> ROTATION_AXIS= 1.0 0.0 0.0
> OSCILLATION_RANGE=0.5 !degrees (>0)
>
> X-RAY_WAVELENGTH=1.14 !Angstroem
> 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
>
> !======================= CRYSTAL PARAMETERS
> =================================
> SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are
> ignored.
> UNIT_CELL_CONSTANTS= 139.53 249.90 119.83 90.000 112.511 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.
>
>
>
>
> However indexed cell parameter for a b and c is small and error
> information indicates that cell solution is not accurate. I suspect that
> I need to change some input parameters besides selection
> of ORGX=3072.0 ORGY=3072 when using XDS as the template is for ADSC Q105.
>
> Here I want to know if anyone has experience to use XDS to process data
> collected at Q315r and what error I made for using this script.
>
> Thank you very much for any suggestion.
>
> Best regards,
>
> Donghui
>
>
--------------------------
Konstantin Korotkov, Ph.D.
Research Scientist
University of Washington
Department of Biochemistry
Box 357742
Seattle, WA 98195-7742
(206)616-4512
[log in to unmask]
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