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 are coloured across the spectral palette so each frame is distinguishable. Use --ensemble-color to choose a different palette or a fixed colour, or pass cpk for standard per-element atom colours.

Default (spectral)	CPK per-element	Viridis + opacity

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

From Python, the ensemble options are passed to load(), which builds the multi-conformer Molecule; render() then draws it:

from xyzrender import load, render

render(load("triphenylbenzol.xyz", ensemble=True))                                          # spectral palette (default)
render(load("triphenylbenzol.xyz", ensemble=True, ensemble_color="cpk"))                    # per-element CPK colours
render(load("triphenylbenzol.xyz", ensemble=True, ensemble_color="#FF0000"))                # single colour
render(load("triphenylbenzol.xyz", ensemble=True, ensemble_color="viridis"), opacity=0.4)   # faded palette
render(load("triphenylbenzol.xyz", ensemble=True, align_atoms=[21, 22, 23]))                # align on subset
render(load("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, comma-separated colours, or cpk for per-element atom colours (default: spectral)
--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)