Phase Studio is a desktop environment for iterative crystallographic phase retrieval, density-map processing, and model preparation. It integrates Superflip, SharpED, and EDMA into a reproducible workflow with direct interoperability with Jana2020.
Phase Studio can be used either with Jana2020 .inflip projects or as a standalone application with external reflection data. Crystallographic metadata can be taken from a Jana .inflip file, a reference structure, or entered manually.
- Superflip charge-flipping and model-seeded reconstruction workflows
- Optional SharpED density-map deblurring
- EDMA peak extraction from raw and processed maps
- HKL validation and resolution-dependent completeness analysis
- Iterative next-cycle model generation
- Optional map symmetrization and map-feedback workflows
- Side-by-side comparison of reference, Superflip, and SharpED-derived structures
- Jana2020 hand-off for selected reconstruction results
- Reproducible storage of generated inputs, maps, models, metrics, and logs
Reflection data
↓
Superflip
↓
XPLOR map
↙ ↘
EDMA SharpED
↓
optional symmetry averaging
↓
EDMA
↓
next-cycle model
↓
Superflip
Selected result → Jana2020
Optional stages are included only when enabled in the workflow.
A ready-to-run Windows build is available from the project releases page:
The packaged Windows application does not require a separate Python installation.
Phase Studio does not redistribute Superflip or EDMA. Install them separately:
Jana2020 is required only for Jana-specific integration, .inflip workflows, and transfer of results back to Jana2020. Standalone external-HKL workflows can be used without an active Jana2020 project.
SharpED processing is optional. Phase Studio can run with Superflip and EDMA alone.
Server-side SharpED processing requires an API token:
The application default SharpED server is:
https://jana.fzu.cz/
- Start Phase Studio.
- Configure the Superflip and EDMA executable paths if necessary.
- Choose an input mode.
- Select the source of crystallographic metadata.
- Use Validate HKL to verify the reflection-data interpretation.
- Use Analyze completeness to inspect resolution-dependent data quality.
- Configure the reconstruction workflow and optional processing steps.
- If SharpED is enabled, enter an API token and select a model.
- Click Run pipeline.
- Inspect convergence, structure comparisons, and generated outputs.
- For Jana2020 workflows, use Send to Jana2020 when the desired result is available.
Use an existing Jana2020 .inflip file as the primary crystallographic input. Phase Studio can obtain crystallographic metadata and compatible Superflip settings from the file.
Use the Jana .inflip file as the workflow template while overriding selected reflection, reference, or configuration inputs in Phase Studio.
Use reflection data prepared outside Jana2020. Crystallographic metadata can be supplied from:
- a compatible reference structure, or
- manual metadata entry.
Manual metadata entry supports unit-cell parameters, space-group information, and composition for HKL-only workflows.
Validate HKL checks how the selected reflection file is parsed and reports, among other items:
- parsed and unique reflection counts,
- σ(Fobs) availability,
- phase-value coverage,
- unit cell and space group,
- a reflection sample with derived quantities.
Analyze completeness provides:
- completeness vs.
sinθ/λ, - mean
I/σ(I)vs.sinθ/λ, - reflection-distribution statistics,
d_min,- the resolution at 98% cumulative completeness,
- resolution-bin statistics.
The main window reports both:
- Overall progress across reconstruction cycles, and
- Current cycle progress through the active workflow stage.
The dashboard also includes:
- Superflip convergence metrics,
- synchronized structure comparison,
- execution log and diagnostics.
- User Manual — complete user-facing reference
- Example Workflows — practical configurations and workflows
- Building Phase Studio — source installation, packaging, and wrapper deployment
Reusable branding assets are stored in phase_studio/assets/: the Windows multi-size phase_studio.ico, square cross-platform phase_studio_icon.svg/.png, and full phase_studio_logo.svg/.png.
Phase Studio is developed at the:
Department of Structure Analysis
Institute of Physics of the Czech Academy of Sciences
- Jiří Zelenka — zelenka@fzu.cz
- Jan Rohlíček — rohlicek@fzu.cz
- Monika Kučeráková
- Zdeněk Buk
General project/support contact:
- Phase Studio source and releases: https://github.com/ji-ze/Phase-Studio
- SharpED: https://sharped.fzu.cz/
- Superflip and EDMA: https://superflip.fzu.cz/
Phase Studio is designed for crystallographic reconstruction and density-map workflows involving diffraction data, electron-density or electrostatic-potential maps, partially solved structures, and iterative model-seeded phase retrieval.
It complements Jana2020 and does not replace crystallographic refinement in Jana2020.