Dear all, Following Pierre and Harry's suggestion, problem solved using xdsme -i 'ROTATION_AXIS= -1.0 0.0 0.0'" image_name_*.img. Thank you very much.
Good luck for everyone Cheers, Donghui On Thu, Dec 9, 2010 at 12:39 AM, LEGRAND Pierre < [email protected]> wrote: > Hi again, > > One last comment, following Harry's suggestion, if the phi axis turns in > the revers order, for xdsme and xds you will need the following command: > > xdsme -i 'ROTATION_AXIS= -1.0 0.0 0.0'" image_name_*.img > > Good luck, > Pierre > > > -----Original Message----- > From: CCP4 bulletin board on behalf of wu donghui > Sent: Wed 12/8/2010 4:40 PM > To: [email protected] > Subject: Re: [ccp4bb] How to use XDS programme to process data collected at > Q315r detector > > Marian, > > It seems that XDS does matter detector type Q315 or Q315r. Same crystals > when collected at ESRF Beamline 23-1 using Q315 detector can be processed > straightly with the provided script from XDS website and I only need to > input ORGX=1536.0 ORGY=1536.0 for indexing or data integration. If XDS > does > not matter Q315 or Q315r, the indexing of data from Q315r should be as > clear > as from Q315 collected at ESRF beamline 23-1. But XDS can not index the > data > from Q315r correctly. > > Best regards, > > Donghui > > > > > ************************************************************ > ***************** > ! 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=1536.0 ORGY=1536.0 !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. > > On Wed, Dec 8, 2010 at 11:05 PM, Marian Szebenyi <[email protected]> > wrote: > > > Donghui, > > > > The Q315r and Q315 have the same format, so for the XDS input it does not > > matter whether you have a Q315 or Q315r. What does matter is whether the > > data were collected in "binned" or "unbinned" mode. For binned, the > number > > of pixels is 3072 and the pixel size is 0.10259 mm. For unbinned, the > number > > of pixels is 6144 and the pixel size is 0.0513. In your case, the file > > header tells you that you have binned data, with 3072 x 3072 pixels and a > > pixel size of 0.10259, and this is the information you need to give XDS. > > > > Yours, > > > > Marian Szebenyi > > MacCHESS > > > > 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] > >> <mailto:[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 > >> > >> > >> > >
