Conformer Ensemble

Visualise multiple conformers from a multi-frame XYZ trajectory overlaid on a single reference frame. Each frame is RMSD-aligned onto the reference (frame 0) via the Kabsch algorithm. By default, conformers render with standard CPK atom colours. Use --ensemble-color to apply a continuous palette or a fixed colour.

Default (CPK)	Viridis + opacity

xyzrender triphenylbenzol.xyz --ensemble -o triphenylbenzol_ensemble.svg
xyzrender triphenylbenzol.xyz --ensemble --align-atoms 21,22,23 --ensemble-color viridis --opacity 0.4 -o triphenylbenzol_ensemble_custom.svg

From Python:

from xyzrender import render

render("triphenylbenzol.xyz", ensemble=True)                                          # CPK colours
render("triphenylbenzol.xyz", ensemble=True, ensemble_color="spectral")               # spectral palette
render("triphenylbenzol.xyz", ensemble=True, ensemble_color="#FF0000")                # single colour
render("triphenylbenzol.xyz", ensemble=True, ensemble_color="viridis", opacity=0.4)   # faded palette
render("triphenylbenzol.xyz", ensemble=True, align_atoms=[21, 22, 23])               # align on subset
render("triphenylbenzol.xyz", ensemble=True, max_frames=10)                          # limit frames

Alignment subset

By default the Kabsch fit uses all atoms. Use --align-atoms to fit on a subset (minimum 3 atoms to define a plane); the rotation is still applied to every atom. This works for both --ensemble and --overlay.

xyzrender triphenylbenzol.xyz --ensemble --align-atoms 21,22,23 -o ensemble_align.svg
xyzrender isothio_xtb.xyz --overlay isothio_uma.xyz --align-atoms 1-6 -o overlay_align.svg

Skip alignment

--no-align disables Kabsch entirely and renders each frame at its raw coordinates, preserving the trajectory’s native geometry. Useful for trajectories where the absolute frame matters.

xyzrender triphenylbenzol.xyz --ensemble --no-align -o ensemble_raw.svg

Flag	Description
--ensemble	Enable ensemble mode for multi-frame XYZ trajectories
--ensemble-color VALUE	Palette name (viridis, plasma, spectral, coolwarm, RdBu, rainbow), a single colour, or comma-separated colours
--opacity FLOAT	Opacity for non-reference conformers (0–1, default: 1.0)
--align-atoms INDICES	1-indexed atom subset for alignment (min 3), e.g. 21,22,23 or 1-6
--align / --no-align	Force / skip Kabsch alignment (default: on)