---
name: DIALS core meeting 2024-06-13
tags: core meeting
---

# DIALS core meeting 2024-06-13

## Previous Actions

- [ ] **ND** Investigate getting `psana` tests running on the DIALS xfel-regression testing
- [ ] **ND**: Investigate using stable-nightly conda builds of cctbx (e.g. cctbx tests) longer term
- [ ] **JBE**: H5 on-disk experiment: review practicalities of using this & welcome people looking at James's work above. round trip example files could be useful - exists in dials.export.
- [x] **ND**: XFEL-regression test failures. Seem to have resolved themselves with time.
- [ ] **ND**: Sync new releases with current state of dials/cbflib and main branch. Keep synced.

## Agenda

### OptionParser
- Dials east has reserved time to look into removing some of the limitations on this. Graeme notes: https://github.com/dials/dials/pull/1265
- Set for Tues 21st
- [https://github.com/dials/dials/compare/main...new-argument-parser](https://github.com/dials/dials/compare/main...new-argument-parser) branch, Ben not cleaned for review yet

### JBE Demos
- Previously [[prev](https://dials.github.io/kb/core/2024-04-04)]:
- Draft PR https://github.com/dials/dials/pull/2567
- GW suggested making a special release in order to test this changeset at DLS (in new year).
- Wait until PR notes addressed, then build this as a test release for wider consumption
- Not been touched much since NY
- Keeps coming up as something that would be useful
- James has rebased this, updated tests, Rick and Kevin feel OK with this => need to pick up some PR comments
- Hope to merge in near future (next month)
- Aaron points to [notes](https://github.com/cctbx/cctbx_project/tree/master/xfel/conda_envs)
- Previous Actions: Still relevant?
- **AB**: Run this against Xfel-regression tests: AB pls can you run this James?
- ~~**ND**: Make test release using these branches~~
- Few more issues outstanding
- 3.19 out now so good time to merge testing - providing xfel-regression works
- Paper taking next two weeks (pick up next time)
- Jun 13th - Still writing, starting to pick up things. Next time should be better.
- H5 Reflection Table PR: https://github.com/dials/dials/pull/2677
- Discussion about shoeboxes

### Making ellipsoid integrated data work with cctbx.xfel.merge
- JBE: I had prepared this, but now I'm not sure this is the best approach, discuss:
https://github.com/dials/dials/pull/2661

Discussion of how to handle the difference between partiality and so on between the DIALS ellipsoid model / xfel.merge postrefine was discussed: since the intensities are modified "it's complicated." Need to make sure not to correct for partiality _twice_. Per-image scale factors are computed before postrefinement but Wilson B is only optimised during postrefinement - so this is meaningfully different from how dials.scale works.

Conclusion: share custom script

One further complication - in cctbx.xfel.merge, only 'outlier rejection' can occur as part of repredictions during postrefinement, so this not available for ellipsoid at moment - probably want to be able to handle ellipsoid integrated data properly in cctbx.xfel.merge, rather than just applying the partiality correction coming out of dials + turning off postrefinement.

### MetaCIF
- Ability to add extra metadata that is merged into the output shelx file in dials.export
- Discussion about `xia2.to_shelx` and xia2 exporting metadata
- Graeme points out xia2 CIF handling in https://github.com/xia2/xia2/blob/main/src/xia2/Handlers/CIF.py
- Dan is not here today. Pick up next week. (if available).
- Take off for now

## AOB?

### Next meeting

Thursday, June 27th, 4pm (BST), 8am (PDT)