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Subject:

Re: How to use XDS programme to process data collected at Q315r detector

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Wed, 8 Dec 2010 16:41:30 +0100

Content-Type:

multipart/signed

Parts/Attachments:

Parts/Attachments

text/plain (226 lines) , signature.asc (226 lines)

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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