A ChimeraX bundle for geometric particle picking in cryo-electron tomography.
Temporary splash image — placeholder, to be replaced.
Source / issues: https://github.com/baradlab/Geopickr · Changelog: CHANGELOG.md
Geopickr brings the subtomogram-averaging picking pipeline into one tabbed ChimeraX tool. It is a fork and port of three UCSF Chimera plugins written by Kun Qu in the laboratory of John Briggs (originally MRC LMB / Heidelberg, now Max Planck Institute of Biochemistry):
- Place Points — mark sphere centers / tube & filament axes on a tomogram (a thin helper over ChimeraX's native marker tools; replaces the Volume Tracer step).
- Geometry Picker — geometrically sample evenly-spaced particle positions and orientations on spheres, tubes, filaments, or arbitrary surface meshes, producing a 20×N TOM/AV3 motive list. (Ports Pick Particle.)
- Place Object — display a motive list as placed objects, colored by class or cross-correlation. (Ports Place Object.)
This bundle ports these tools from UCSF Chimera to UCSF ChimeraX, integrates
them into a single tabbed interface, and adds new functionality (a filament
mode, arbitrary-surface picking, live per-object radius fitting, instanced
rendering, and STOPGAP .star export). It supersedes the original Chimera
plugins Place Object 2.1.0 and Pick Particle 2.0.0.
This is an independent, community fork. It is not produced or endorsed by the Briggs laboratory or UCSF. Please cite the original work (below) in any publication that uses this tool.
Original author: Kun Qu, Briggs laboratory. The original plugins are distributed under the GPL v3 and are described in:
- Place Object — Qu K., Glass B., Dolezal M., Schur F.K.M., Murciano B., Rein A., Rumlova M., Ruml T., Kräusslich H.-G., Briggs J.A.G. (2018) Structure and architecture of immature and mature murine leukemia virus capsids. PNAS 115:E11751–E11760.
- Pick Particle — Qu K., Ke Z., Zila V., Anders-Oesswein M., Glass B., Mücksch F., Müller R., Schultz C., Müller B., Kräusslich H.-G., Briggs J.A.G. (2021) Maturation of the matrix and viral membrane of HIV-1. Science 373:700–704.
The original Place Object / Pick Particle plugins remain © their authors and are
GPL v3; portions of the original code carry the UCSF Chimera copyright. This fork
preserves that licensing (see License). Geometry assets (src/objects/*.stl)
are carried over from the original Place Object plugin.
- Chimera → ChimeraX port (Qt UI instead of Tkinter; native ChimeraX models, sessions, and commands).
- Single tabbed tool (ArtiaX-style) instead of three separate windows.
- New geometry modes: Filament (centerline + tangent orientation + optional helical twist) and Surface (area-weighted, Poisson-thinned sampling of any open OBJ/PLY/STL mesh). Sphere and Tube are faithful ports of Qu's maths.
- Live radius fitting — a single whole-model radius slider by default, or per-object sliders, updating the fit wireframes in real time.
- Efficient instanced rendering — one
Surface+Placesper motive list, scaling to tens of thousands of particles. - STOPGAP
.starexport in addition to.em.
From source:
ChimeraX --nogui --exit --cmd "devel install /path/to/ChimeraX-Geopickr exit true"
or, once released, from the ChimeraX Toolshed (Tools → More Tools…) or:
toolshed install ChimeraX-Geopickr
Then open it from Tools → Volume Data → Geopickr — one window with Place Points, Geometry Picker, and Place Object tabs.
- Place Points tab: New marker set → Mark on plane → right-click VLP centers in the tomogram.
- Geometry Picker tab: select the marker set → Sphere → set the Radius slider and Tangential spacing → Show fit (optionally tick Per-object radii) → Pick.
- The particles appear in the Place Object tab; adjust shape/color and
Save shown… as
.emor STOPGAP.star.
Command equivalent:
open spheres.cmm
pickparticle #2 style sphere radius 50 tangential 10
See the in-app help (help:user/tools/pickparticle.html) for full details of the
motive-list format and every control.
Geopickr currently reads and writes the formats used by the original Briggs-lab pipeline:
| Purpose | Format | Read | Write |
|---|---|---|---|
| Markers (sphere centers / tube & filament axes) | Chimera marker XML (.cmm) |
✓ | ✓ (via the Markers tool) |
| Surface meshes for surface picking | any surface ChimeraX can open (.obj, .ply, .stl, volume isosurfaces, …) |
✓ | — |
| Motive list (particle positions/orientations) | TOM/AV3 EM (.em), 20×N matrix |
✓ | ✓ |
| STOPGAP star | STOPGAP (.star) |
— | ✓ |
| Dynamo table | Dynamo (.tbl) + optional volume-list (.vll) hand-off |
— | ✓ (beta) |
| RELION 5 | RELION 5.1 particles star (centered Å, rlnTomoSubtomogram*) |
— | ✓ (beta) |
| RELION 3/4 | RELION 3/4 tomo star (pixel coords, rlnAngleRot/Tilt/Psi) |
— | ✓ (beta) |
Use Export… in the Place Object or Geometry Picker tab, or the command
geopickr export #model file <path> format <em|stopgap|dynamoTbl|relion5|relion3> [onTomogram #vol] [tomoId n] [tomoName name] [vll <path>].
Coordinate units: Dynamo
.tblneeds voxel indices and RELION needs voxel/centered-Å coordinates, but Geopickr's particles live in ChimeraX scene units. Choose the source tomogram Volume in the Export dialog (oronTomogram) so coordinates are converted correctly (voxel size, box dimensions, origin read from the map). Without a Volume the coordinates are assumed to already be in voxels.
Beta: the Dynamo/RELION angle conventions are cross-validated against ArtiaX (Geopickr's exported Euler angles reproduce the same particle orientation through ArtiaX's own
DynamoEulerRotation/RELIONEulerRotation). The coordinate-origin conventions (Dynamo 1-indexing, RELION 5 centering at box/2) follow ArtiaX/standard usage but have not yet been confirmed against a live Dynamo/RELION import on real data. Please report mismatches (issues #1, #2) with an example.
The 20-row .em motive-list layout follows the TOM/AV3 convention (CCC, tomogram
/feature indices, X/Y/Z coordinate + shift, ZXZ Euler angles, class); see the
in-app help for the exact rows.
We want Geopickr to fit as many subtomogram workflows as possible. If your
pipeline uses a coordinate/orientation format that isn't supported yet (e.g. a
different .star flavour such as RELION/Warp/M, Dynamo .tbl, IMOD .mod,
EMAN .json, plain text, …), please open an issue at
https://github.com/baradlab/Geopickr/issues with:
- a short description of the format and the tool/pipeline it comes from,
- a small example file (and, if relevant, the matching output it should produce), and
- the coordinate and angle conventions (handedness, units, rotation order, whether shifts are separate from coordinates).
Concrete examples make it far easier to add a format correctly, and we'd love to grow the list of supported import/export options.
GPL v3, following the original Place Object / Pick Particle plugins. See LICENSE.