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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 ...
= 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 and email?''

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.

== Setting up ==
=== Image Location ===

It is not recommended to process the images from within the same directory as the images are. At least create a subdirectory. In many cases the data images are on an external disk or remotely mounted directory with an awfully long path name.
If you images are "/some/where/with/a/very/long/path", [[XDS.INP]] may not find the images and one must create a link to the actual directory.
<pre> #> ln -s /some/where/with/a/very/long/path images </pre>.

=== Getting [[XDS.INP]] ===
You must know the type of detector your data were collected on. Then visit the [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html|XDS Homepage], download the appropriate template and rename it to [[XDS.INP]].

== Editing [[XDS.INP]] ==
This tutorial uses the template for XDS-MARCCD.INP.

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 aus is [http://www.scripps.edu/~arvai/adxv.html adxv]: It allows to view the image header where these numbers often can be found. [[Image:Adxv_menu.jpeg|100px|adxv image viewer, main menu]] [[Image:Adxv_pixelsize.jpeg|100px|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|200px|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).
#'''Experiment specific settings''' The following numbers are also usually found in the image header:
DETECTOR_DISTANCE= 150.0 !(mm)
OSCILLATION_RANGE=1.0 !degrees (>0)
X-RAY_WAVELENGTH=1.07176 !Angstroem
NAME_TEMPLATE_OF_DATA_FRAMES=./images/tutorial_????.img ! TIFF
DATA_RANGE=1 180 !Numbers of first and last data image collected
#'''Background range''' The default template suggests to use the first 5 images for detecting the average background per image. It does not harm to increase this number to 20 images. Especially with frame width of less than 1 degree you should do this.
BACKGROUND_RANGE=1 20 !Numbers of first and last data image for background

This is it to start. type <pre>#> xds_par </pre> to run xds and wait until it's finished.
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