View source for Tutorial(First Steps)

= 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]] and running XDS is explained. 

There is also a [[generate_XDS.INP|script]] that sets up XDS.INP automatically, at least for common types of detectors. Much easier than setting up and running XDS manually should be the usage of [[XDSGUI]].

== 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 your images are at a path with embedded blanks, e.g. "/my/USB disk/path", XDS is not able to access the images and one must create a link to the actual directory: 
 #> ln -s "/my/USB disk/path" images 

=== Getting [[XDS.INP]] ===
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]] ==
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): 

* '''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).
* '''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)
 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
 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.