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 <[log in to unmask]> 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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