I don't see the job card in your script. So it will assume job= all and then it is more than normal that xds will complain about the indexing being inaccurate. Look at the idxref.lp file and pick your space group then rerun xds adding job=devpix See what happens Am on my phone will send you my script later Jürgen
...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Dec 8, 2010, at 9:53, wu donghui <[email protected]> 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 >
