Examples

Each example is a directory under examples/ holding its input files and a spec.yaml. The links for each example go to the directory that produced it.

Every view carries its own caption, rendered from the Markdown file its title_md names.

Antigenic regions of influenza H3 hemagglutinin

Five views of one structure, each with its own CSV saying how to color each site. Switch between them with the View selector below the structure: only the first view pins a camera, so whatever you frame there stays framed through the rest.

Open the above view on a new page

Rendered from examples/8faw_antigenic_regions/ with:

prot-struct-viz spec.yaml

file	what it is
spec.yaml	the whole input: five views sharing one YAML anchor
antigenic-regions-w-glycans.csv	every modeled residue and every glycan, coloring antigenic regions
antigenic-regions.csv	the same without the glycan rows, which is what lets this view's glycans: hide take them away
perth-2009-to-subclade-k.csv	the sites that differ between the two HAs, plus the sialic-acid receptor analogue. Everything unnamed falls back to default_color
2025-26-to-2026-27-vaccine.csv	a shorter list of sites
subclade-k-with-region-d-mutations.csv	the sites of the view above, plus HA1 222 and 223 in a different color
antigenic-regions-w-glycans.md, antigenic-regions.md, perth-2009-to-subclade-k.md, 2025-26-to-2026-27-vaccine.md, subclade-k-with-region-d-mutations.md	the caption for each view
make_coloring_csv.py	generates all five CSVs from a numbering map

Antigenic regions of influenza H1 hemagglutinin

The same five views over the asymmetric unit rather than a biological assembly: 9GSP deposits all three protomers, so the asymmetric unit is already the trimer and there is no symmetry for Mol* to expand. Every CSV here therefore names each protomer in turn.

Open the above view on a new page

Rendered from examples/9gsp_antigenic_regions/ with:

prot-struct-viz spec.yaml

file	what it is
spec.yaml	the full input spec
antigenic-regions-w-glycans.csv	every modeled residue of all three protomers, and every glycan, coloring antigenic regions
antigenic-regions.csv	the same without the glycan rows, which is what lets this view's glycans: hide take them away
california-2009-to-d-3-1.csv	the sites that differ, once per protomer. Everything unnamed falls back to default_color
d-3-1-to-d-3-1-1.csv	the sites that differ, once per protomer
d-3-1-1-with-g155e.csv	those sites plus site 155 in a different color, again once per protomer
antigenic-regions-w-glycans.md, antigenic-regions.md, california-2009-to-d-3-1.md, d-3-1-to-d-3-1-1.md, d-3-1-1-with-g155e.md	the caption for each view
make_coloring_csv.py	generates all five CSVs

Influenza B neuraminidase active site

A handful of hand-picked residues instead: insertion-coded author numbering, a ligand and a glycan colored from the CSV rather than by element, and a per-chain base representation. It is also the one example rendered with style: illustrative, and the one that opens with Mol*'s own panels showing rather than closed.

Open the above view on a new page

Rendered from examples/1f8b_active_site/ with:

prot-struct-viz spec.yaml

file	what it is
spec.yaml	the whole input: one view over the biological tetramer
coloring.csv	hand-written rows, some asking for a drawn label. Its notes column shows how to keep an explanation beside a residue while label stays short enough to draw — unrecognized columns are ignored
chains.csv	the per-chain base representations, for chain_representation
title.md	the caption below the viewer