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v0.4.0 – 3D buttons, compare, FSC curves, MCP server

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@LUKASinScience LUKASinScience released this 17 Oct 18:37
· 5 commits to main since this release
v0.4.0
56d4b12

Highlights

  • 3D buttons. Every job that holds a map gets a 3D chip (and a Mask chip). Maps open in one ChimeraX window, handed over through a private folder: no network port. reliontree ships its own listener, so the ChimeraX-InstantMap plugin is optional.
  • Settings for clusters. Set how ChimeraX is started, including a Run first line such as module load chimerax, and an optional FigureStyle template for opened maps. Changes from the page need a per-run token and a matching Host/Origin.
  • Command line. New compare (jobs side by side: resolution, particles, maps, changed options, class overlap), maps, open and settings.
  • Resolution (FSC) in the job details from postprocess.star or run_model.star; the orientation globe also works from run_data.star when a job has no *_angdist.bild.
  • reliontree mcp: a read-only MCP server (stdio) for AI assistants: list_jobs, job_info, lineage, why, diff, methods.
  • A new guide with install options (environment, cluster module, no install): https://lukasinscience.github.io/reliontree/
  • Also: reliontree.start_background() to embed the live view in another program, contrib/chx_run.py (whitelisted headless ChimeraX calls with JSON results), contrib/cryosparc/cs2relion.py (CryoSPARC to RELION through pyem's csparc2star, with a validator), and tests on GitHub Actions (Python 3.9 / 3.11 / 3.13, Linux and macOS).

Fixed

  • Long classifications (hundreds of run_itNNN_class*.mrc) lost their 3D buttons because the folder looked like a data dump; iteration maps no longer count towards that limit.

Install

pip install "git+https://github.com/LUKASinScience/reliontree@v0.4.0"

(Python 3.9 or newer, no further dependencies.)

Known limits

  • Developed and tested on macOS; Windows is untested.
  • The MCP server has been exercised with a test client, not yet with every assistant.
  • The resolution marked in the FSC plot is interpolated and can differ from RELION's shell value by up to one shell.
  • The CryoSPARC helper is tested with synthetic files, not yet with a real export.
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