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.
• 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 branch, Ben not cleaned for review yet

JBE Demos

• Previously [prev]:
  • 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
• 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)