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
k...@u.washington.edu
--------------------------
