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(New page: = A beginner's walk-through to XDS = ''This page is under development. If you think it might be useful to you and worth completing faster, why not simply bother the author by sending him ...) |
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= A beginner's walk-through to XDS = | = A beginner's walk-through to XDS = | ||
This tutorial is directed at people who are beginners to XDS and do not want to start reading about all the technical details but rather want their images processed. Other processing programs are often more attractive to new users because using a GUI make starting easier than a [[XDS.INP|script file]]. If you notice a mistake or gap in this tutorial, please contact the authors. | |||
In the following, the manual mode of setting up XDS.INP is explained. But there is also a [[generate_XDS.INP|script]] that does most of this automatically, at least for common types of detectors. | |||
== Setting up == | == Setting up == | ||
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=== Getting [[XDS.INP]] === | === Getting [[XDS.INP]] === | ||
You must know the type of detector your data were collected on. Then visit the [http:// | You must know the type of detector your data were collected on. Then visit the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html XDS Homepage], download the appropriate template and rename it to [[XDS.INP]]. | ||
== Editing [[XDS.INP]] == | == Editing [[XDS.INP]] == | ||
This tutorial uses the template for XDS-MARCCD.INP. | This tutorial uses the template for XDS-MARCCD.INP (templates can be downloaded from [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html]. | ||
Open [[XDS.INP]] with your favourite text editor (e.g. gedit, kate, kwrite, vim, emacs...) and make the following adjustments (from top to bottom): | Open [[XDS.INP]] with your favourite text editor (e.g. gedit, kate, kwrite, vim, emacs...) and make the following adjustments (from top to bottom): | ||
* '''Pixel Size''' Find out the number of pixels of your detector. A very good program to find this is [http://www.scripps.edu/~arvai/adxv.html adxv] (also see the wiki article [[adxv]]): It allows to view the '''image header''' where these numbers often can be found. [[Image:Adxv_menu.jpeg|200px|adxv image viewer, main menu]] [[Image:Adxv_pixelsize.jpeg|300px|adxv showing image header info. Pixel size is highlighted]] | |||
* '''Adjusting JOB Card''' Make a copy of the '''JOB''' line in [[XDS.INP]] for reference. Comment out one line by putting a exclamation mark "!" at the beginning of the line and prepare the other one to run the steps from XYCORR to CORRECT.[[Image:XDS_INP_adjustingJOB.jpeg|400px|Adjusting the JOB card in XDS.INP]] | |||
* '''ORGX and ORGY''' Unless you can guess the direct beam position on the images, ''e.g.'' from ice rings, set both these values to half the detector size. In the case of this example, where the MAR-CCD is 3072x3072 pixels, this means | |||
ORGX=1536.00 ORGY=1536.00 !Detector origin (pixels). | ORGX=1536.00 ORGY=1536.00 !Detector origin (pixels). | ||
* '''Experiment specific settings''' The following numbers are also usually found in the image header (or in your lab notebook, or in logs written by the beamline software): | |||
DETECTOR_DISTANCE= 150.0 !(mm) | DETECTOR_DISTANCE= 150.0 !(mm) | ||
OSCILLATION_RANGE=1.0 !degrees (>0) | OSCILLATION_RANGE=1.0 !degrees (>0) | ||
X-RAY_WAVELENGTH=1.07176 !Angstroem | X-RAY_WAVELENGTH=1.07176 !Angstroem | ||
NAME_TEMPLATE_OF_DATA_FRAMES=./images/tutorial_????.img ! TIFF | NAME_TEMPLATE_OF_DATA_FRAMES=./images/tutorial_????.img ! TIFF | ||
DATA_RANGE=1 | DATA_RANGE=1 180 !Numbers of first and last data image collected | ||
#''' | SPOT_RANGE=1 90 !images to be used for indexing; 1 180 would be better unless there is radiation damage | ||
Then data processing can start. type <pre>#> xds_par </pre> to run xds and wait until it's finished. | |||
== Indexing Fails == | |||
If the detector origin is too far from the image centre, IDXREF is going to stop with the error message | |||
!!! ERROR !!! SOLUTION IS INACCURATE | |||
Do the following: | |||
* In IDXREF.LP, find the table '''INDEXING OF OBSERVED SPOTS IN SPACE GROUP''' | |||
***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP # 1 ***** | |||
16196 OUT OF 76452 SPOTS INDEXED. | |||
0 REJECTED REFLECTIONS (REASON: OVERLAP) | |||
60256 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION) | |||
EXPECTED ERROR IN SPINDLE POSITION 2.398 DEGREES | |||
EXPECTED ERROR IN DETECTOR POSITION 1.72 PIXELS | |||
Unless really hardly any reflections could be indexed (second line in the table), scroll a few lines up and copy the refined values for the beam origin | |||
DETECTOR ORIGIN (PIXELS) AT 1514.16 1537.27 | |||
as improved ORGX and ORGY to [[XDS.INP]] and try indexing again. | |||
XDS is quite robust and in many cases this approach works. If not, read [[Obtaining ORGX ORGY]]. | |||
* Check the refined detector distance | |||
DETECTOR ORIGIN (PIXELS) AT 1514.16 1537.27 | |||
CRYSTAL TO DETECTOR DISTANCE (mm) 422.92 | |||
If it deviates by more than 1-2mm from the input distance, check all your parameters again. Is the wavelength really correct, as well as the distance? If you are sure about them, try indexing with only a few images | |||
SPOT_RANGE = 1 20 | |||
== See also == | |||
[https://{{SERVERNAME}}/pub/MWhitley_CSHL-2018_XDS-Tutorial.pdf Matthew J. Whitley's excellent tutorial] about XDS processing with [[XDSGUI]], from the 2018 Cold Spring Harbor X-Ray Methods in Structural Biology Course. | |||