Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

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 <
pierre.legr...@synchrotron-soleil.fr> 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: CCP4BB@JISCMAIL.AC.UK
> 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 11101010 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 trans

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

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  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/ 
>
> 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 11101010 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

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Bosch, Juergen]

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/

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 11101010 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 

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Tim Gruene]

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 11101010 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  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.
> >
> > !***

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

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 11101010 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  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:

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Jürgen Bosch]

I don't see the job card in your script.
So it will assume job= all and then it is more than normal that xds will 
complain about the indexing being inaccurate. Look at the idxref.lp file and 
pick your space group then rerun xds adding job=devpix
See what happens
Am on my phone will send you my script later
Jürgen 

..
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/

On Dec 8, 2010, at 9:53, 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 11101010 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  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

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Harry Powell]

Hi

I think the phi rotation on that beamline is the opposite way round to most 
other Q315s - so in Mosflm you'd need to have a "DETECTOR REVERSEPHI" line (or 
click the "reverse direction of spindle rotation" box in iMosflm). I don't know 
what you'd do in XDS, but I don't think there is anything in the header (apart 
from the detector serial number) that would give a clue about it. You just need 
to know about the individual detector.

There's no reason why images from a Q315r should be less easy to process than 
those from a Q315 in XDS or Mosflm. I'd stick with Mosflm, personally, but 
you'd expect me to say that. 

On 8 Dec 2010, at 14:53, 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 11101010 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  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
> 
>  DETE

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

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 11101010 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  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 11101010 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);

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Konstantin v. Korotkov]

Donghui,

there are several ways to get ORGX ORGY parameters. As Juergen suggested, 
you could use the numbers from the header or Mosflm output.

More information on the excellent XDS Wiki:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Obtaining_ORGX_ORGY

Another option would be to run generate_XDS.INP script, which will get 
ORGX ORGY parameters from headers automatically:

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP

If you know the spacegroup, define it with keyword SPACE_GROUP_NUMBER= 
(your script has 0).


HTH,
Konstantin

On Wed, 8 Dec 2010, wu donghui 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




--
Konstantin Korotkov, Ph.D.

Research Scientist
University of Washington
Department of Biochemistry
Box 357742
Seattle, WA 98195-7742

(206)616-4512
k...@u.washington.edu
--

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Jürgen Bosch]

Look into the header of your image file via more or run mosflm on one image and 
look at the output in the terminal window.

You'll get the pixelsize and you'll need to convert the beamcenter into pixels 
from mosflm. Keep in mind that beam X = orgy in xds and beam y is orgx
Plus the usual stuff lambda distance 2theta

Jürgen 

..
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/

On Dec 7, 2010, at 22:03, wu donghui  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 11101010 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

[ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

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 11101010 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