2,652
edits
Tutorial(First Steps): Difference between revisions
Jump to navigation
Jump to search
→Editing XDS.INP
| Line 20: | Line 20: | ||
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|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). | 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. | Then data processing can start. type <pre>#> xds_par </pre> to run xds and wait until it's finished. | ||