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Phase Studio 1.0.4 for Jana2020

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@ji-ze ji-ze released this 17 Aug 03:53
· 11 commits to main since this release
v1.0.4
f944409

Phase Studio 1.0.4 for Jana2020

Phase Studio 1.0.4 is a major user-interface and workflow update focused on reliable iterative crystallographic reconstruction, clearer diagnostics, and tighter integration of Superflip, SharpED, EDMA, and Jana2020.

This release provides a standalone Windows one-file executable and supports both Jana2020-based workflows and reconstruction from external reflection data.

02_iterative_workflow_dashboard

Monitor iterative Superflip, SharpED, and EDMA processing with normalized convergence metrics, synchronized structure views, two-level progress, and a structured execution log.

Highlights

  • Redesigned scientific desktop interface with separate Basic and Advanced configuration levels
  • Support for Jana .inflip, external HKL, reference-structure, and manual crystallographic-metadata workflows
  • Integrated HKL Validation for checking reflection parsing, metadata, phase coverage, and uncertainty columns
  • New HKL Completeness analysis with:
    • completeness vs. sinθ/λ
    • mean I/σ(I) vs. resolution
    • reflection-distribution statistics
    • d_min
    • resolution at 98% cumulative completeness
    • resolution-bin statistics and export
  • Iterative Superflip workflows with configurable next-cycle models
  • XPLOR damping for model-seeded reconstruction
  • Optional SharpED density-map processing with server-side model discovery
  • Automatic SharpED element handling from composition
  • Integrated EDMA peak extraction from raw and processed maps
  • Optional processed-map symmetrization
  • Optional map-feedback workflows
  • Normalized Superflip convergence dashboard
  • Synchronized comparison of Reference, Superflip, and SharpED structures
  • Improved pipeline monitoring with separate overall and current-cycle progress
  • Consistent READY, RUNNING, COMPLETE, CANCELLED, and ERROR states
  • Improved cancellation and recovery behaviour
  • Structured execution log with clearer workflow and diagnostic messages
  • Updated built-in Help, README, User Manual, and example workflows

HKL completeness analysis

Phase Studio 1.0.4 includes a dedicated resolution-dependent data-quality view for evaluating completeness and signal before or alongside reconstruction.

05_hkl_completeness

The HKL Completeness view provides:

  • symmetry-aware reflection completeness
  • completeness vs. sinθ/λ
  • mean I/σ(I) vs. resolution
  • reflection-distribution statistics
  • d_min
  • resolution at 98% cumulative completeness
  • median I/σ(I)
  • phase-value coverage
  • σ(Fobs) coverage
  • shell-by-shell resolution statistics
  • CSV and plot export

The current diagnostic view is designed to combine resolution limits, signal quality, and reflection statistics in one exportable interface.

HKL validation

Reflection-data interpretation can be checked before the reconstruction starts.

04_hkl_validation

The validation dialog reports:

  • selected reflection source and format
  • unit cell and space group
  • parsed and unique reflection counts
  • phase-value coverage
  • σ(Fobs) coverage
  • reflection-column interpretation
  • individual reflection records
  • derived I/σ(I), d, and sinθ/λ values

This provides a direct way to detect incorrect reflection formats, column interpretation, or crystallographic metadata before launching a reconstruction.

SharpED integration

SharpED processing is fully integrated into the Phase Studio workflow but remains optional.

03_sharped_configuration

Phase Studio can:

  • authenticate against the configured SharpED server
  • query available server-side models
  • select the SharpED model
  • derive elements automatically from the active composition
  • configure output-map sampling
  • control upload-size limits
  • configure HTTP timeout and polling behaviour
  • download processed density maps directly into the reconstruction workflow

The SharpED configuration is integrated directly into the same workspace used for Superflip and EDMA processing.

A SharpED API token is required only when SharpED processing is enabled.

SharpED and API-token access:

https://sharped.fzu.cz/

Default Phase Studio SharpED server:

https://jana.fzu.cz/

Input and metadata workflows

Phase Studio 1.0.4 supports several ways to define a reconstruction.

Jana .inflip

Use an existing Jana2020 .inflip file as the primary crystallographic input.

Jana .inflip with overrides

Use a Jana .inflip file as the workflow template while overriding selected reflection, reference, or configuration inputs.

External HKL

Use reflection data prepared independently of Jana2020.

Crystallographic metadata can be supplied from:

  • a reference structure
  • Jana input where applicable
  • manual unit-cell, symmetry, and composition entry
01_paths_and_metadata

Configure reflection sources, crystallographic metadata, reference models, working directories, and external programs from one validated workspace.

Iterative reconstruction workflow

A typical Phase Studio reconstruction can combine:

Reflection data
      ↓
  Superflip
      ↓
   XPLOR map
   ↙      ↘
 EDMA    SharpED
           ↓
  optional symmetry averaging
           ↓
          EDMA
           ↓
    next-cycle model
           ↓
       Superflip

Selected result → Jana2020
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