easYPipe ‘reindex’

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

The program try to reindex according to the space group of 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
sg_ref space group of reference for reindexing (name or number)

Example:

$ easypipe.py PROCESSED_DATA reindex P41212
equivalent to:
$ easypipe.py PROCESSED_DATA reindex 92

What does it do ?

_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_reindexed.csv’ in ‘/easypipe/1b_reindex…’ folder, with reindexed mtz files information
_images/mtz-to-treat-ALL-csv_NEW1.jpg

becomes:

_images/csv-reindex_NEW2.jpeg

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. Even if they don’t need to be reindexed, you have to run ‘reindex’ step to have the right reindexed csv file including these new datasets.