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Geopickr 1.1.0b1 (beta)

Geopickr 1.1.0b1 (beta) Pre-release
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@bbarad bbarad released this 19 Jun 20:59
v1.1.0b1
4fd6e24

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

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Geopickr 1.0.0

Geopickr 1.0.0 Latest
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@bbarad bbarad released this 18 Jun 03:30
v1.0.0
1276c32

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.

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