toolwatch-2026-05-15.md

CryoCore Toolwatch 2026-05-15

This note records current useful tools, repos, services, and preprints for BioSymphony CryoCore. It is a triage document, not approval to install, run, or redistribute any gated software, model weights, raw movies, maps, or private data.

Decision Rules

• planned means useful enough for docs, manifests, smoke checks, or public-safe adapters after normal license/source review.
• gated means public docs and placeholders are useful, but execution, packaging, upload, or redistribution needs an explicit operator/license gate.
• watch means scientifically relevant but not yet a dependable production dependency for evidence closeout.
• Provider status and ML-generated outputs are not evidence by themselves. Claims still require input joins, tool versions, hashes, validation artifacts, and caveats.

Highest Value Additions

Area	Candidate	Posture	Why it helps CryoCore	Source
Atomic model building	CryoAtom2	planned	MIT repo; protein, RNA, DNA, masked local builds, sequence-free and sequence-DB modes; newer complement to ModelAngelo.	https://github.com/YangLab-SDU/CryoAtom
Atomic model building	DiffModeler / ComplexModeler	gated	Intermediate-resolution complex modeling with diffusion tracing and predicted-model fitting; Kihara licensing requires use-context review.	https://github.com/kiharalab/DiffModeler
Atomic model building	CryoREAD	gated	Dedicated nucleic-acid model building for cryo-EM maps.	https://kiharalab.org/emsuites/cryoread.php
Model quality	DAQ score / DAQ refine	gated	Residue-wise map/model compatibility scores for claim ledgers; local code/assets need exact terms review.	https://kiharalab.org/emsuites/daq.php
Validation	3D-Strudel	planned	Apache-2.0 map-feature validation around 2-4 A; useful local outlier panels.	https://www.ebi.ac.uk/emdb/strudel
Validation	EMDA	planned	MPL-2.0 map/model FSC, local correlation, difference-map utilities.	https://emda.readthedocs.io/en/latest/index.html
Validation	MapQ / Q-score	planned/gated	MIT plugin; public reports can be parsed, local recompute inherits Chimera/ChimeraX posture.	https://github.com/gregdp/mapq
Validation	wwPDB / RCSB validation APIs	planned/gated	Public validation report ingestion for released entries; upload of unpublished/private files needs explicit approval.	https://www.wwpdb.org/validation/validation-reports
Heterogeneity	DynaMight	planned	RELION 5 flexibility lane with deformation/backprojection evidence; complements cryoDRGN/RECOVAR.	https://github.com/3dem/DynaMight
Heterogeneity	CryoBench	planned	Benchmark datasets and metrics for state/ensemble claim calibration.	https://cryobench.cs.princeton.edu/
Heterogeneity	SOLVAR	watch	2026 covariance/pose-refinement method; repo exists but license must be clarified before packaging.	https://arxiv.org/abs/2602.17603
Preprocessing	nextPYP	planned	End-to-end cryo-EM/ET workflow platform with Apptainer/HPC fit; dependencies need individual gates.	https://nextpyp.app/
Preprocessing	CTFFIND5	planned/gated	Improved CTF/tilt/thickness estimation; redistribution posture must be checked before image inclusion.	https://elifesciences.org/articles/97227
Preprocessing	cisTEM	planned/gated	Independent SPA pipeline and cross-check lane; Janelia terms must be recorded.	https://cistem.org/
Preprocessing	Scipion/Xmipp	planned/gated	Provenance, format conversion, many plugin integrations; plugin execution remains mixed-license.	https://scipion-em.github.io/docs/release-3.0.0/
Preprocessing	pyem / csparc2star	planned	High-leverage metadata conversion between cryoSPARC and RELION.	https://github.com/asarnow/pyem
Preprocessing	AreTomo3	planned	Real-time cryoET tilt-series preprocessing/reconstruction.	https://github.com/czimaginginstitute/AreTomo3
Preprocessing	MicrographCleaner	planned	Contamination/carbon mask helper before picking and QC.	https://github.com/rsanchezgarc/micrograph_cleaner_em
Public data	EMPIAR REST API	planned	Public raw-data metadata and accession checks without storing raw assets.	https://www.ebi.ac.uk/empiar/
Public data	EMDB REST API / EMICSS	planned	Map metadata, validation-analysis pointers, cross-resource annotations.	https://www.ebi.ac.uk/emdb/api/
Public data	RCSB PDB Data API	planned	Structure metadata, validation report fields, GraphQL/REST enrichment for dossiers.	https://data.rcsb.org/
Visualization	MolViewSpec	planned	Declarative Mol* scenes for reproducible web dossiers.	https://academic.oup.com/nar/article/53/W1/W408/8125619
Visualization	py3Dmol / 3Dmol.js	planned	Lightweight notebook/static HTML molecular panels.	https://3dmol.org/
Visualization	open-source PyMOL	planned	Scripted publication figures without Incentive license files.	https://github.com/schrodinger/pymol-open-source
Workflow	Nextflow	planned	Provider-neutral profiles for local, Slurm, AWS Batch, cloud, and containers.	https://github.com/nextflow-io/nextflow
Workflow	Snakemake	planned	Python-native local/HPC reproducibility for smaller demos and fixtures.	https://github.com/snakemake/snakemake
Workflow	Apptainer	planned	HPC-safe container runtime with SIF hashes for non-Docker environments.	https://github.com/apptainer/apptainer
Provenance	RO-Crate / BagIt / SBOM / SLSA	planned	Durable evidence bundles, fixity manifests, and container provenance.	https://www.researchobject.org/ro-crate/

Gated But Useful

• CryoSPARC and CryoSPARC Live remain high-value production tools, but runtime and commercial use are gated. cryosparc-tools can be a planned metadata adapter if its BSD-3-Clause posture is pinned.
• Phenix remains the canonical gated refinement/validation suite. Expand docs around phenix.validation_cryoem, phenix.map_to_model, phenix.predict_and_build, phenix.real_space_refine, and mtriage.
• ChimeraX remains gated but should be treated as a scripted renderer/review runtime: .cxc scripts, --offscreen, saved .cxs, Toolshed bundle inventory, exact version, and command ledger.
• CCP-EM/Buccaneer, VMD/NAMD/MDFF, crYOLO, RECOVAR current main, and Kihara suite tools need exact per-campaign use-context records.
• Large model weights for CryoAtom, ModelAngelo, CryoFM, Cryo-IEF, CryoWizard, and similar tools belong in runtime caches, volumes, or reviewed image layers with hashes, never in git.

Preprints And Watchlist

These are worth tracking, but should not close scientific claims without independent validation and license/runtime review.

Candidate	Why watch	Why not productionize yet	Source
CryoFM	Apache-2.0 density foundation model for denoising, inpainting, anisotropy correction, and style enhancement.	Foundation-model outputs can alter apparent map quality; require explicit derived-map caveats and weight hashes.	https://github.com/ByteDance-Seed/cryofm
Cryo-IEF / CryoWizard / CryoDECO	Foundation model for image evaluation plus automated processing/ranking pipelines.	Interfaces with CryoSPARC and large weights; needs tool-by-tool license and evidence-gate review.	https://github.com/westlake-repl/Cryo-IEF
CryoNet.Refine	2026 diffusion refinement preprint/code claims faster model-map refinement.	Needs local reproducibility, stereochemistry stress tests, and license confirmation.	https://arxiv.org/abs/2602.22263
PhenixCraft	2026 preprint for AlphaFold-assisted Phenix map segmentation/model building.	Preprint stage; determine whether it is a method pattern or a distributable tool.	https://arxiv.org/abs/2605.05259
CryoHype	Large-scale compositional heterogeneity with transformer hypernetworks.	Research benchmark method; not an operator-ready evidence lane.	https://cryohype.cs.princeton.edu/
CryoPANDA	Large annotated particle dataset preprint for data-driven cryo-EM analysis.	Dataset size and redistribution/access terms need review; use metadata pointers first.	https://preprints.epiforecasts.io/paper/10.64898/2026.04.29.720997
CryoFSL	Few-shot SAM2 particle picking.	Model/data terms and local smoke tests needed before planned status.	https://pmc.ncbi.nlm.nih.gov/articles/PMC12458156/
CryoSift	CNN 2D class selection and automated processing workflow.	Validate code/packaging and avoid over-trusting class rank output.	https://journals.iucr.org/f/issues/2025/12/00/ih5009/
CryoFastAR	Fast ab initio reconstruction, but noncommercial/split licensing.	License blocks public/default runtime use.	https://github.com/Cellverse/CryoFastAR
CryoGEM / GEM / CryoGS	Neural/Gaussian reconstruction representations.	Method-development watch; not yet a default raw-to-map evidence lane.	https://github.com/Cellverse/CryoGEM

Repo Actions

1. Keep references/software-registry.yaml broad but conservative: add planned entries only for tools with clear public source/terms and immediate CryoCore value; use gated or watch when in doubt.
2. Add workflow provenance contracts: workflow engine/version/ref, executor, profile, container runtime, trace path, image digest or SIF hash, SBOM path, and tool versions.
3. Split map/model validation into explicit outputs: geometry, global FSC, model-map FSC, local CC, Q-score/Strudel/SMOC-like local metrics, deposition report IDs, source hashes, and caveats.
4. Add public accession metadata helpers for EMPIAR, EMDB, PDBe, RCSB, and wwPDB validation reports. These should emit JSON ledgers and never download raw movies or maps unless an operator gate allows it.
5. Add reusable repo-local skills so future agents can repeat toolwatch, closeout, map/model dossier, heterogeneity, and figure workflows with the same planned/gated/watch discipline.