These tutorials assumes the steps outlined in setup have been followed first. Processing xfel data at LCLS consists of four steps:
- Averaging and other Preparatory steps
- Metrology refinement
- Indexing and integration. Optional steps:
- Advanced Merging: Use cases for isomorphous replacement and de novo structure
- cctbx.prime: Merging using the prime.postrefine program.
- Resolving an Indexing Ambiguity
Additionally, cctbx.xfel utilizes phil files to manage its configuration settings.
Processing L498 thermolysin details instructions to reproduce the results published in the forthcoming cctbx.xfel paper.