Phase Studio 1.0.6

Phase Studio 1.0.6 hides the beta/experimental SharpED phasing methods behind an opt-in toggle, fixes a stale warning message and a convergence graph that went dead partway through a phase-recycling run, reorganizes the Basic settings tabs so each one holds a single, clear group of controls, and splits Help into a Basic guide and an Advanced guide that each explain every control on their own tabs.

This release provides standalone one-file executables for Windows and Linux. No separate Python installation is required.

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Highlights

• Beta and experimental phasing methods are now hidden by default, not just labeled — a new opt-in setting reveals them
• Fixed the Phasing method warning message not reliably appearing/disappearing when switching methods
• Fixed the convergence graph going flat after cycle 1 during SharpED phase recycling — a new Map correlation metric tracks every cycle
• New Recommended starting preset, applied by default
• Basic tabs reorganized into Input → Workflow → Output → Help, each holding one coherent group of settings
• Map format gains two reflection-file export options: HKL reflections with phases and ShelX (fcf)
• Every dropdown menu now opens at the same, more compact size instead of varying from one control to the next
• Help is now split into a Basic guide and a new Advanced guide, each explaining every control on its own tabs

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New: opt-in visibility for beta/experimental features

Advanced → Setup → Interface has a new checkbox, Show beta and experimental features in settings, unchecked by default. While it's off, the two SharpED phase-recycling phasing methods and the Symmetrize (beta) option are removed from the Basic tabs entirely — not grayed out, not present. Turning it on makes them selectable again; turning it back off while one is active safely falls back to standard Superflip.

Alongside this, the two methods are now named and worded more precisely:

• 1st Superflip, then SharpED (beta) — warns that it doesn't work well with some models.
• SharpED (experimental) — renamed from "SharpED (beta)"; warns that it doesn't work well yet and is intended for development, not production use.

Fixed: warning message and convergence graph during phase recycling

• The Phasing method warning callout could fail to show or hide reliably when switching methods, because its visibility was read back from Qt after being set, which layout state could get wrong. It now uses a single source of truth for the decision.
• The convergence graph previously went flat after cycle 1 whenever a SharpED phase-recycling method was selected, because every plotted metric came from Superflip's own log — and Superflip runs at most once in these methods. A new Map correlation metric (each cycle's recomposed map compared with the previous cycle's, requiring no reference structure or EDMA) now gives real per-cycle feedback and is written to metrics.csv.

New: Recommended starting preset

Workflow preset is renamed Starting preset and gains a Recommended entry — a general-purpose baseline (cycles 5, Superflip, deblurred XPLOR next-cycle model, XPLOR damping 0.3, SharpED model "koala 2.0", all optional processing except symmetry averaging) that is now the default selection, matching the built-in defaults on a fresh install. The sample-type presets (MOF atomic/medium resolution, small molecule, inorganic) and custom are unchanged.

Reorganized: Basic tabs and Map format

• Basic → Model is gone. "Reference and initial model" moved to Input; the SharpED Model selector moved to Workflow; the remaining working-directory/format settings are now their own Output tab.
• Map format (Basic → Output) gains HKL reflections with phases and ShelX (fcf), replacing the separate "Save standardized HKL" checkbox — both save the observed reflections instead of an extra density map. Existing settings with that checkbox on carry over automatically.
• Every dropdown menu across the app now opens with the same compact row height instead of some being noticeably taller than others.

Split: Help now has a Basic guide and an Advanced guide

The single Help tab is now two: Basic → Help covers the Basic tabs (getting-started guide, plus new Input/Workflow/Output reference sections explaining every control there, and About); Advanced → Help is a new tab covering Setup/Superflip/EDMA/SharpED/Map feedback, each expanded into an exhaustive per-control reference, plus the raw Superflip keyword reference. "Open guide" buttons and F1 context help jump to the correct one automatically.

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Full Changelog: v1.0.5...v1.0.6

Phase Studio 1.0.5

Phase Studio 1.0.5 adds an experimental phase-recycling reconstruction path built around SharpED, a resumable pipeline, and a substantial cleanup of the Basic/Advanced settings so the everyday controls are easier to find.

This release provides standalone one-file executables for Windows and Linux. No separate Python installation is required.

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Highlights

• New beta phasing methods that recycle phases through SharpED instead of repeating Superflip every cycle
• Continue button to resume a stopped or finished run exactly where it left off
• Superflip's referencefile is now filled in automatically from cycle 2 onward, fixing electron-density map drift when no reference file is selected
• Redesigned Map format / Structure format output controls, replacing a confusing set of overlapping checkboxes
• Reorganized Basic tabs (Input → Workflow → Model → Help) and Advanced tabs (Setup → Superflip → EDMA → SharpED → Map feedback) so the most-used controls are easiest to reach
• New "universal" default settings for a smoother first run
• Several correctness fixes, including a map-blur bug in the new recycling algorithm

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New: SharpED phase-recycling phasing methods (beta)

Basic → Workflow → Phasing method now offers two additional options alongside the standard Superflip cycle:

• 1st Superflip, then SharpED (beta) — Superflip runs only once, on cycle 1. From then on, every cycle deblurs the previous map with SharpED, calculates phases by FFT from that deblurred map for every measured reflection (expanded over the full space-group symmetry), and recomposes a map from the observed |Fobs| amplitudes with those phases. That recomposed map is what SharpED deblurs next cycle.
• SharpED (beta) — the same recycling loop, but skips Superflip entirely: cycle 1 starts from a map synthesized directly from |Fobs| with independent random phases. This can take extremely long to converge, even for simple structures (hundreds of cycles), and convergence is not guaranteed.

Both methods can optionally run EDMA once, on the final cycle's map, via a new Run EDMA on final map option. Selecting either method automatically disables the Superflip-cycle-specific controls (Next-cycle model, XPLOR damping, Symmetrize processed map, per-cycle EDMA) that don't apply to it.

New: Continue

Continue resumes the previous run — whether it was stopped gracefully, stopped immediately, or simply finished — reusing the same crystal metadata, reflections, and cycle-to-cycle feedback instead of starting over. If the previous run already reached its configured number of cycles, raise Cycles above the completed count before continuing.

Improved: Superflip referencefile handling

Without a reference file, Superflip has no fixed origin in reciprocal space relative to the previous cycle, so the electron density map can drift. From cycle 2 onward, when no reference file is selected, Phase Studio now automatically supplies one: the most recent EDMA CIF from the previous cycle, or that cycle's XPLOR map if EDMA produced no usable peaks. Cycle 1, and any run with an explicitly selected reference file, are unaffected.

Improved: Output format selection

The previous pile of overlapping checkboxes (legacy auxiliary outputs, save XPLOR/CCP4/Jana map, export Jana2020 project) and a separate Superflip output-format field are now two single-choice dropdowns on Basic → Model → Output:

• Map format: xplor / xplor + ccp4 / xplor + Jana (m80/m81)
• Structure format: cif / cif + xyz / cif + pdb

XPLOR and CIF remain mandatory internal working files for Superflip, EDMA and SharpED regardless of the chosen extra format — nothing about the underlying reconstruction changed, only how the export choice is presented. The redundant "Export Jana2020 project" option was removed; the real "Send to Jana2020" hand-off is unaffected.

Reorganized settings

• Basic: Input (data + crystal metadata) → Workflow (reconstruction settings, now with a visually grouped Optional processing section) → Model (reference/initial model, SharpED model choice, output settings) → Help.
• Advanced: Setup (Superflip/EDMA executable paths, SharpED server URL and API token) → Superflip → EDMA → SharpED (elements, resolution, network/upload) → Map feedback (now flagged with a warning that it rewrites observed reflection data, not just the model).
• Beta and experimental features are labeled (beta) directly on their controls, not just in a tooltip.
• New default settings on a fresh install: Cycles 5, Next-cycle model deblurred XPLOR, XPLOR damping 0.3, SharpED model "koala 2.0", and refreshed Superflip defaults (2000 iterations, repeat mode 10, automatic random seed, final polish enabled, symmetry-based best densities, minimum value/σ 2.0, atom-based normalization).

Fixes

• The Run button now consistently reads "Run phasing"; it previously reverted to a stale "Run pipeline" label after a stop, error, or completed run.
• Fixed a bug in the new phase-recycling methods where recomposed maps only used each measured reflection's own reciprocal-lattice position instead of its full space-group-symmetry-equivalent set, producing a heavily smeared map instead of a properly reconstructed one for any space group beyond P1/P-1.
• Fixed an internal bug where selecting "1st Superflip, then SharpED" could silently behave like the random-phase-start "SharpED" method instead.

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Full Changelog: v1.0.4...v1.0.5

Phase Studio 1.0.4 for Jana2020

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.

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

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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

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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.

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.

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HKL validation

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

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.

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SharpED integration

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

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/

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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

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

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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

v1.0.3

Full Changelog: v1.0.2...v1.0.3

v1.0.2

Full Changelog: v1.0.1...v1.0.2

1.0.1

Full Changelog: v1.0.0...v1.0.1

Phase_Studio_for_Jana_Win64

Nusnost nakopírovat místo superflipu do složky s nainstalovaným programem Jana2020. Funguje na Windows 11