Thanks Tim, our mails must have crossed :-) @ Donghui: This is the standard JOB card JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT what you probably need is after running the first time xds in the directory to go back into your script and change it into JOB=DEFPIX XPLAN INTEGRATE CORRECT And also change the space group and unit cell according to the output in IDXREF.LP
Jürgen Alternatively is the geometry of your beamline the same as in the script ? DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 - 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/<http://web.me.com/bosch_lab/> On Dec 8, 2010, at 10:41 AM, Tim Gruene wrote: 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 <wdh0...@gmail.com> 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
