Use case "Indexing with XDS"

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Summary

This use case describes indexing performed by XDS.

In XDS, there are three steps requiered before autoindexing:

  • XYCORR: Calculates lookup tables of spatial corrections if needed (CCD detector images are usally already corrected).
  • INIT: Evaluation of the images (gain and background)
  • COLSPOT: Collection of spots on one or a list of images.

The autoindexing step IDXREF can than be run.


Importance Important
Priority High priority
Use Frequency Not frequently used
Direct Actors Kernel
Pre-requirements Kernel running

Input

In XDS Information between the steps is communicated by files that have a fixed name. This makes it mandatory to process each data set in a newly created directory to avoid name clashes. At startup, XDS lookup for the "XDS.INP" text file that contains all the input parameters. Commentary can be added afer a "!".

Required

Example of minimum input for the XYCORR step (needed, even if there is no spacial correction to apply).

 JOB= XYCORR 
 DATA_RANGE= 1 75
 DETECTOR= ADSC
 NX= 3072    NY= 3072    QX= 0.1026    QY= 0.1026   
 ORGX= 1629.0    ORGY= 1533.4

Example of minimum input for the INIT step.

 JOB= INIT 
 DATA_RANGE= 1 75
 DETECTOR= ADSC
 NX= 3072    NY= 3072    QX= 0.1026    QY= 0.1026   
 ORGX= 1629.0    ORGY= 1533.4
 
 BACKGROUND_RANGE= 1 5
 NAME_TEMPLATE_OF_DATA_FRAMES= ../62-1_1_???.img

Example of minimum input for the COLSPOT step.

 JOB= COLSPOT
 DATA_RANGE= 1 75
 DETECTOR= ADSC
 NX= 3072    NY= 3072    QX= 0.1026    QY= 0.1026   
 ORGX= 1629.0   ORGY= 1533.4   
 BACKGROUND_RANGE= 1 5
 NAME_TEMPLATE_OF_DATA_FRAMES= ../62-1_1_???.img

 SPOT_RANGE= 1 6
 SPOT_RANGE= 70 75

Note: In most case, the beam center coordinate (ORGX and ORGY) is reversed in X/Y compared to the standard ESRF definition. These coordinates are expressed in pixels.

Example of minimum input for the IDXREF step.

 JOB= IDXREF
 DATA_RANGE= 1 75
 DETECTOR= ADSC
 NX= 3072    NY= 3072    QX= 0.1026    QY= 0.1026   
 ORGX= 1629.0    ORGY= 1533.4
 BACKGROUND_RANGE= 1 5
 NAME_TEMPLATE_OF_DATA_FRAMES= ../62-1_1_???.img   
 SPOT_RANGE= 1 6
 SPOT_RANGE= 70 75

 OSCILLATION_RANGE= 1.0   
 STARTING_ANGLE= -175.0   
 STARTING_FRAME= 1   
 X-RAY_WAVELENGTH= 1.04   
 DETECTOR_DISTANCE= 450.0   
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0   
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0   
 ROTATION_AXIS= 1.0 0.0 0.0   
 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0   

Optional

Output

Required

Optional

Main Success Scenario

Variations

Notes and Questions