Using Untangle to filter overlapping reflections

You may use either the driver scripts for batch processing of diffraction data, or the GUI for interactive visualisation of the data.

Using Denzo to index separate patterns

The crystal orientation is defined by the crystal rotx, roty and rotz parameters.
  1. Start XDisplayF and load a suitable image.
  2. Run a peak search. This creates a file called peaks.file.
  3. Start Denzo and run autoindexing. With luck, this will converge on a first orientation. NOTE: it may be necessary to experiment to find the best frame and number of peaks for optimal autoindexing.
  4. Perform any necessary refinement steps and write a x file (for instance data_1_001.x) containing the spots identified for the first orientation.
  5. Run peaksfilter data_1_001.x. This will eliminate from peaks.file all peaks that have been associated with the first orientation by the first Denzo run.
  6. Start Denzo again and rerun the autoindexing procedure. With more luck, a second orientation will now be identified.
  7. Repeat steps 3-6 as needed.
You should now have a set of processing parameters for each subcrystal, which can be used to process all frames and generate the individual datasets.

Using MOSFLM to index separate patterns:

In MOSFLM, it is necessary to select an appropriate set of peaks for autoindexing to find the correct orientations. This generally requires some trial and error.

Using ScalePack to combine data from different orientations

The following example scalepack.com file combines data from three different crystal orientations:
scalepack <<eof-sclpck |tee scalepack.log
number of zones 10

[ Detector-specific settings ]
estimated error 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07

[ Crystal-specific settings ]
resolution 25.0 2.8
error scale factor 1.7
rejection probability 0.001
space group 19   [ P2(1)2(1)2(1) ]

[ Refinement options ]
reference batch 10
postrefine 10
scale restrain 0.05
b restrain 0.3

fit crystal a*  1 to 120 121 to 240 241 to 360
fit crystal b*  1 to 120 121 to 240 241 to 360
fit crystal c*  1 to 120 121 to 240 241 to 360

fit crystal mosaicity  1 to 120 121 to 240 241 to 360
add partials           1 to 120 121 to 240 241 to 360

[ Data input ]
format DENZO_ip

sector 1 to 120
file 1 'filtered_1_###.x'

sector 1 to 120
file 121 'filtered_2_###.x'

sector 1 to 120
file 241 'filtered_3_###.x'

[ Data output ]

write rejection file 0.9
output file filtered123.sca