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 ?¶


- 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

becomes:

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.