Data Processing

Most data processing utilities (with the exception of HKL2000) should be run from a "Data Processing" console. Simply double-click the "Data Processing" icon on the desktop. There is a separate icon for running HKL2000 (see below).

Viewing Images

• To view your diffraction images (.img files) or their header information, follow the instructions found in the Viewing Images section.

XDS and Autoprocess

• Visit the XDS Home Page.
• Using XDS is made easy at the CMCF through an in-house autoprocess script which generates the appropriate input files and runs XDS. It uses POINTLESS to identify the space group from systematic absences and BEST to create a data collection strategy. A new directory is created that contains the input and output files. A summary of the processing is contained in a file named 'process.log'.
• Autoprocess is invoked by typing:
  autoprocess [options] [image_file.img]
  For example, to process a native dataset with autoprocess, in the directory with the image files type:
  autoprocess any_image_file.img
  To process an anomalous dataset, type:
  autoprocess -a any_image_file.img
  To obtain a strategy for a native data collection, collect 5 degrees of data then type:
  autoprocess -s first_image_file.img
  To obtain a strategy for an anomalous data collection, collect 5 degrees of data then type:
  autoprocess -a -s first_image_file.img
  Finally, to see the full list of options, including options for processing MAD datasets, type:
  autoprocess
  without any arguments.

• Autoprocess does not take full advantage of all the features of XDS. For example, there may be some instances when the user may want XDS to try a different spacegroup than the one suggested by the autoprocess input file. A full list of the XDS input parameters is available on the XDS website.
• In these cases, XDS may be invoked directly by typing xds, but suitable input files must be prepared before it can be used.
• It is recommended to first run autoprocess on your image files to obtain appropriate input files, then modify them appropriately.
• An example of an input file appears below:

  !-XDS.INP-----------File generated by autoxds
  JOB=ALL
  MAXIMUM_NUMBER_OF_PROCESSORS=16
  MAXIMUM_NUMBER_OF_JOBS=2
  MINUTE=0
  !-------------------Dataset parameters-------
  X-RAY_WAVELENGTH=0.97934
  DETECTOR_DISTANCE=150.0
  OSCILLATION_RANGE=1.00
  SPACE_GROUP_NUMBER=75
  UNIT_CELL_CONSTANTS=    77     77     38   90   90   90
  !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0
  NAME_TEMPLATE_OF_DATA_FRAMES=images/Gd_Lysozyme_1_E0_????.img TIFF
  DATA_RANGE=1 190
  SPOT_RANGE=1 5
  !-------------------Beamline parameters----- 
  NX=3072    NY=3072 
  QX=0.07324 QY=0.07324 
  ORGX=1512  ORGY=1537
  
          DETECTOR=CCDCHESS
          MINIMUM_VALID_PIXEL_VALUE=0    
          OVERLOAD=65000
          TRUSTED_REGION=0.02 1.35
          VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000
          ROTATION_AXIS= 1.0 0.0 0.0
          INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
          FRACTION_OF_POLARIZATION=0.95
          POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
          DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
          DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
          AIR=0.00033
         
  !-------------------File generated by autoxds

• (Note that autoprocess was formerly also known as autoxds, a name that has since been adpoted at SSRL. Although the old name may still appear in some documentation, it is not to be confused with anything in use at SSRL.)

HKL2000

• As described on its website, "HKL-2000 program package is based on the extended versions of Denzo, XDisplayF and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc."
• View the online HKL2000 manual here.
• HKL2000 is started from the HKL2000 icon on the desktop.



• Running HKL2000 off-site with data collected at CMCF will require a site file corresponding to one of the following detectors:
  • 08ID-300 for the MarCCD 300 currently in use at beamline 08ID-1
  • 08ID-225 for the MarCCD 225 which was in use at beamline 08ID-1 before April 2010
  • 08B1-300HE for the MarCCD 300HE currently in use at beamline 08B1-1

Mosflm

• Mosflm is started by typing imosflm. Alternatively, Mosflm can be run from the command line by typing ipmosflm.
• View the online Mosflm user guide here.