Geopickr 1.1.0b3 (beta)

Added

• Pick with an offset — a new Offset (voxels) field in the Geometry Picker
  moves particles along their own +Z axis (surface normal for sphere/tube/surface,
  axis tangent for filament) as they are picked, baked into the coordinates.
  Show fit previews it for sphere/tube as a cyan "particle shell" at
  radius + offset (outside the yellow fit for positive, inside for negative).
  Also on the command: pickparticle … offset <voxels>.
• Bake the Place Object Z/phi offset into exports — the Export dialog and
  geopickr export gain an "apply display offset" option (default on), so an
  offset dialed in for viewing can be folded into the exported coordinates.
  Two independent knobs: bake at pick time, and/or tweak later and bake at export.

Fixed

• STOPGAP .star compatibility — bare column tags (dropped the RELION-style
  #1, #2, … suffixes STOPGAP does not expect) plus a blank line between the
  loop header and the data. Matches STOPGAP's own stopgap_star_write.m; without
  the blank line STOPGAP's reader would drop the first particle.

Builds on 1.1.0b2. Dynamo/RELION export angle conventions remain ArtiaX-validated;
coordinate origins are still pending live-import confirmation (issues #1, #2).

Install: download the wheel and, in ChimeraX:
toolshed install /path/to/chimerax_geopickr-1.1.0b3-py3-none-any.whl

Geopickr 1.1.0b2 (beta)

Incorporates the ChimeraX RBVI Toolshed review feedback and UI density work.

Changes since 1.1.0b1

• Floating window + compact spacing — Geopickr opens as its own floating
  window (not docked) with tightened control spacing.
• Denser 2-column layouts — the Object, Sampling and Utilities sections pair
  controls onto shared rows to cut vertical space (helps on laptop screens).
• Help button — added at the bottom of the tool; opens the documentation.
• Clearer command errors — pickparticle reports "No markers were
  specified" / "No surface was specified" instead of an internal traceback.
• US spelling throughout the UI, docs and code.
• Docs — corrected "how to open" text to use the Geopickr menu entry
  and its tabs.

Carries forward 1.1.0b1's Dynamo/RELION export (issues #1, #2 — still
pending live-import testing) and the Place Object first-motl fix (#3).

Install: download the wheel and, in ChimeraX:
toolshed install /path/to/chimerax_geopickr-1.1.0b2-py3-none-any.whl

Geopickr 1.1.0b1 (beta)

Beta pre-release adding multi-format particle export, plus a Place Object fix.

New: export to Dynamo & RELION (issues #1, #2 — pending live-import testing)

• Dynamo .tbl (+ optional .vll volume-list > table reference).
• RELION 5.1 (centered-Å, rlnTomoSubtomogram*) and RELION 3/4 (pixel) star.
• Plus existing .em / STOPGAP .star.
• Export… button in the Place Object and Geometry Picker tabs, and a
  geopickr export command. Coordinates are converted from ChimeraX scene units
  using a chosen tomogram Volume (voxel size / box / origin).
• Angle conventions are cross-validated against ArtiaX (exported Dynamo/RELION
  Euler angles reproduce the same orientation via ArtiaX's own rotation classes).

Fixed

• Place Object: the first opened motive list now has editable visualization
  controls immediately (previously locked until a second list was opened). (#3)

Beta: Dynamo/RELION angle conventions are ArtiaX-validated; the
coordinate-origin conventions (Dynamo 1-indexing, RELION 5 box/2 centering)
still need confirmation against a real Dynamo/RELION import. Please report issues
with example files.

Install: download the wheel and, in ChimeraX:
toolshed install /path/to/chimerax_geopickr-1.1.0b1-py3-none-any.whl

Geopickr 1.0.0

First public release of Geopickr — a ChimeraX bundle for geometric particle
picking in cryo-electron tomography.

One tabbed tool with Place Points, Geometry Picker, and Place Object:
mark sphere centres / tube & filament axes, geometrically sample evenly-spaced
particle positions and orientations on spheres, tubes, filaments, or arbitrary
surface meshes, and display the resulting TOM/AV3 motive list. Export .em or
STOPGAP .star.

Install

Download the wheel below and, in ChimeraX:

toolshed install /path/to/chimerax_geopickr-1.0.0-py3-none-any.whl

Then open Tools → Volume Data → Geopickr. (A Toolshed listing is planned so
this can be installed directly from within ChimeraX.)

Attribution

A fork and port of the UCSF Chimera Place Object (2.1.0) and Pick
Particle (2.0.0) plugins by Kun Qu in the Briggs laboratory. Please
cite the original work (PNAS 2018 115:E11751–E11760; Science 2021 373:700–704).
Independent community fork, not endorsed by the Briggs lab or UCSF. GPL v3.