Dear Donghui, only because XDS shows a warning about an inaccurate solution does not necessarily mean that it did not index your data correctly.
Check the file IDXREF.LP (from bottom to top - log-file are usually more interesting that way round). There should be a summary of the refined values and also a listing of the number of spots XDS could index based on that solution. If the detector distance was NOT refined to a value to far from what it really was and if the number of indexed spots, say, about 40-50% of the total number of spots, just carry on an see whether XDS does not 'click in' to the correct solution. You carry on be going to the JOB-card in XDS.INP and delete all entries before DEFPIX You find an example of what I am talking about at the XDS wiki at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Tutorial(First_Steps) Maybe this helps, Tim On Wed, Dec 08, 2010 at 10:53:33PM +0800, wu donghui wrote: > Dear all, > > Thank you very much for your valuable inputs. This is an update based from > the suggestions. > > Following Pierre's suggestion, I installed xdsme ( > http://code.google.com/p/xdsme/) and run it. xdsme extracts image header as > the below: > > Image format: adsc > Detector type: ADSC 315 > Detector distance: 480.00 mm > X-ray wavelength: 1.1397 A > Oscillation range: 0.5000 degree > Beam coordinate X: 1535.3 pixel > Y: 1535.3 pixel > > As the detector type should be ADSC 315r, the indexing shows warning > information that !!! WARNING in IDXREF. Solution is inaccurate. > > Based on Miles's suggestion, I run the program adxv ( > http://www.scripps.edu/~arvai/adxv.html) to extract image header as the > below: > > Distance 480.000 mm > Pixel Size 0.10259 mm > Wavelength 1.13967 A > Beam Center X: 1535 pixels > Y: 1536 pixels > OSC_RANGE 0.5000 degree > > However the beam center pixel seems to indicate that ccd detector is Q315 > but not Q315r based on the provided template script from XDS website 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 > > > In summary, I can not index my data collected at Q315r Taiwan 13B1 beamline > using XDS program. It seems that XDS process data from Q315 is more > efficient that from Q315r. > > Any suggestions will be much appreciated. > > Best regards, > > Donghui > > > > > > On Wed, Dec 8, 2010 at 11:03 AM, wu donghui <[email protected]> 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 > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
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