Dear Bosch,
Ye, at the moment, I don't know if the geometry of my beamline 13B1 at
Taiwan take the same direction as in the script. How can I get this
information? Directly ask beamline scientists at Taiwan? or if there is some
log files which may contain such information during data collection. Thank
you very much.
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
Best regards,
Donghui
On Thu, Dec 9, 2010 at 12:07 AM, Bosch, Juergen <[email protected]> wrote:
> 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 <[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
>
>
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> phone: +49 (0)551 39 22149
>
> GPG Key ID = A46BEE1A
>
>
>
