easYPipe ‘reindex’

This optional step is useful when several mtz should be in higher symmetry space group.

The program tests alternative indexing schemes to find which one best matches the reference mtz.

Example: P422 can be re-indexed to P41212.

Usage

easypipe.py data reindex [-h] ref_mtz

arguments description
-h, –help show this help message and exit
ref_mtz mtz file of reference for reindexing (mandatory)

Example:

$ easypipe.py PROCESSED_DATA reindex my-ref.mtz

What does it do ?

  • try to reindex mtz file with Pointless [1] if space group is different from reference space group
_images/reindex-summary1.jpg _images/reindex-summary2.jpg
  • launch xtriage [2] for each successfully reindexed mtz to get resolution, completeness, space group and cell parameters
  • write a new ‘mtz_to_treat_ALL.csv’ with reindexed mtz files information
_images/mtz-to-treat-ALL-csv_NEW1.jpg

becomes:

_images/csv-reindex_NEW.jpg

where P422, P4212 processed data have been successfully reindexed to P41212 space group.

Warning

If you run again ‘prep’ step for any reason like adding new datasets, you will have to run again this ‘reindex’ step. Only new datasets will be reindexed, and even if they don’t need to be reindexed, you have to run ‘reindex’ step to have the right csv file for other datasets.