Skip to content

Phase Studio 1.0.5

Choose a tag to compare

View all tags
@ji-ze ji-ze released this 25 Aug 11:48
v1.0.5
af12d42
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

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.

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

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.

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

Assets 4
Loading