latent_traverse_view
Step through an ensemble's conformations as a contoured trajectory, holding contour level at a constant absolute value so density changes remain visible across frames.
Instructions
Step through an ensemble's conformations as a contoured trajectory.
Refuses when the generating method was never identified. That is SPEC invariant I2 working, not a failure: cryoDRGN's latent density can bear no relation to the truth while 3DVA's frames are linear interpolations no particle occupied, and rendering both the same way asserts something for one that holds only for the other.
The contour is held at a constant ABSOLUTE value and converted to each frame's own sigma. PyMOL normalises every map independently on load, so a fixed sigma level would contour each frame at its own scale and flatten away the density change the traversal exists to show.
No latent scatter and no density estimate are drawn, deliberately. In a 41-submission blind challenge most methods missed a genuinely present middle state, so an empty region of latent space is a region of unknown occupancy — never evidence that a conformation does not occur.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | Prefix for the isosurfaces (defaults to "<ensemble>_surf") | |
| color | No | One colour for every frame; a per-frame spectrum would encode frame index as if measured | skyblue |
| level | No | Contour level. If omitted, 1.5 sigma against the first frame is used. | |
| units | No | Units of `level`: "sigma" (read against frame 1) or "absolute" | sigma |
| build_movie | No | Wire the frames to PyMOL's movie timeline so they can be stepped and played | |
| ensemble_name | Yes | An ensemble previously loaded through the load_ensemble tool |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |