jbrowse-plugin-protein3d 0.13.2 → 0.15.0

package/README.md

@@ -1,40 +1,81 @@
 # jbrowse-plugin-protein3d
 
-This is a 3-D protein structure viewer for JBrowse 2
+A 3-D protein structure viewer for JBrowse 2, linked residue by residue to the
+genome.
+
+![TP53 beside PDB 1TUP, p53's core domain bound to DNA, with the R248 hotspot selected](https://raw.githubusercontent.com/GMOD/jbrowse-plugin-protein3d/readme-figure/readme.png)
+
+TP53 beside PDB 1TUP, p53's core domain bound to DNA. R248, a cancer hotspot, is
+selected in magenta on the structure, and its codon is marked on the gene.
+[Open this session](https://jbrowse.org/code/jb2/main/?config=test_data/protein3d_config.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22ProteinView%22%2C%22structures%22%3A%5B%7B%22pdbId%22%3A%221TUP%22%2C%22initialResidues%22%3A%7B%22start%22%3A248%2C%22end%22%3A248%7D%7D%5D%2C%22transcriptId%22%3A%22NM_000546.6%22%2C%22sideBySide%22%3Atrue%2C%22zoomToBaseLevel%22%3Afalse%2C%22colorScheme%22%3A%22mapped-chain%22%2C%22connectedView%22%3A%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr17%3A7%2C673%2C700-7%2C674%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-ncbiRefSeq%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%7D%2C%22clinvar_ncbi_hg38%22%5D%7D%7D%5D%7D).
+CI re-renders the figure from `main` every hour
+([scripts/readme-figure.mjs](scripts/readme-figure.mjs)).
+
+Right-click a gene and choose to open its protein structure. The plugin looks up
+the AlphaFold model through UniProt, lists the experimental PDB entries SIFTS
+maps to that UniProt entry, and can search Foldseek for related structures. It
+aligns each structure to the transcript's translation, so hovering a residue
+highlights its codon and hovering a codon highlights its residue.
+
+## Try it
+
+The [protein browser](https://staging.genomes.jbrowse.org/protein-browser/)
+takes a gene name and opens it in JBrowse with its structure linked to the
+genome. The plugin is also installed by default on
+[genomes.jbrowse.org](https://genomes.jbrowse.org), so it works for any species
+there.
+
+## Documentation
+
+Using the plugin:
+
+- Tutorials on jbrowse.org:
+  [TP53 from prediction to crystal](https://jbrowse.org/jb2/docs/tutorials/tp53_structures/)
+  opens an AlphaFold model and two crystal structures superposed beside the
+  gene, and reads the R248 hotspot back to its codon;
+  [Proteins on genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_proteins/)
+  launches a structure and an MSA from any gene's right-click menu.
+- [Demos](docs/demos.md): structures that are easy to map wrong, each one link
+  away — a peptide bound to a larger partner, a protein bound to DNA, a receptor
+  with another protein fused into it, a phosphorylated residue, and a
+  mitochondrial protein.
+- [Your own structures](docs/your-own-structures.md): opening a model you folded
+  yourself (ColabFold, AlphaFold 3, Boltz…) instead of the AlphaFold DB one,
+  from a file, a URL or a generated link per gene, and which features carry
+  over.
+
+Linking and embedding:
+
+- [Launching from a URL or code](docs/launching.md): worked session-spec links,
+  the short `uniprotId`/`pdbId` + `transcriptId` form, several structures in one
+  view, and the `LaunchView-ProteinView` extension point.
+- [Launch parameters](docs/launch-parameters.md): every argument, the
+  `connectedView` settings, and the transcript `feature` shape.
+- [Session snapshots](docs/session-snapshots.md): the saved view's shape, the
+  structure shorthands, and which chain maps.
+
+How it works, for someone extending the plugin or checking what a number on
+screen means:
 
-The major workflow enabled by this is
-
-- Right click gene of interest -> launch 3-D protein viewer with linked
-  mouseover between genome and structure
-
-It has features to automatically look up a protein structure of interest using
-the UniProt ID mapping API to connect to AlphaFoldDB, lists the experimental PDB
-entries SIFTS maps to that UniProt entry, and can also use Foldseek to look up
-related structures
-
-## Coordinate-mapping harness
-
-A standalone diagnostic page that loads real PDB / AlphaFold structures through
-the plugin's actual mapping code and surfaces cases it mishandles (multi-chain
-complexes, partial/repeat structures, AlphaFold fragments):
-
-https://gmod.org/jbrowse-plugin-protein3d/
-
-Source and details in [harness/](harness/).
-
-## Screenshot
-
-![](img/1.png)
-
-Example at
-https://jbrowse.org/code/jb2/latest/?config=%2Fucsc%2Fhg38%2Fconfig.json&session=share-aZOIjR_qs4&password=NT4sa
+- [Genome to structure alignment](docs/genome-to-structure-alignment.md): why
+  the plugin aligns the transcript's translation to the structure on the fly,
+  the precedent for that in SIFTS and G2S, how it picks the chain and isoform,
+  and what sequence alignment cannot decide.
+- [UniProt feature tracks](docs/uniprot-feature-tracks.md): where the accession
+  and the UniProt-to-structure offset come from for AlphaFold models, PDB
+  entries and your own models.
+- [Residue numbering](docs/residue-numbering.md): how a paper's R248 becomes
+  position 154 in the file, `label_seq_id` 155 for Mol\*, and the codon on
+  chr17, and how a session spec names a residue the literature's way.
 
-## Demos
+Working on the plugin:
 
-[Structures that are easy to map wrong](docs/demos.md), each one link away: a
-peptide bound to a larger partner, a protein bound to DNA, a receptor with
-another protein fused into it, a phosphorylated residue, and a mitochondrial
-protein.
+- [DEVELOPERS.md](DEVELOPERS.md): running it locally and publishing.
+- [Testing](docs/testing.md): the unit, e2e, documentation and demo checks.
+- [Host compatibility](docs/host-compatibility.md): keeping the published bundle
+  working on JBrowse releases years old.
+- [Live checks](docs/live-checks.md): serving a local build to a session on
+  jbrowse.org.
 
 ## Publication
 
@@ -46,33 +87,3 @@ Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal
 of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645
 
 See also https://github.com/GMOD/proteinbrowser for overview
-
-## Availability
-
-This plugin is installed by default on https://genomes.jbrowse.org so you can
-use it on any species there
-
-## Programmatic usage
-
-See [DEVELOPERS.md](DEVELOPERS.md)
-
-## How it works
-
-Notes on the parts that are easy to get subtly wrong, written for someone
-extending the plugin or checking what a number on screen means:
-
-- [Genome to structure alignment](docs/genome-to-structure-alignment.md): why
-  the plugin aligns the transcript's translation to the structure on the fly,
-  the precedent for that in SIFTS and G2S, how it picks the chain and isoform,
-  and what sequence alignment cannot decide.
-- [Residue numbering](docs/residue-numbering.md): how a paper's R248 becomes
-  position 154 in the file, `label_seq_id` 155 for Mol\*, and the codon on
-  chr17, and how a session spec names a residue the literature's way.
-
-## Publishing
-
-just push a new tag using e.g.
-
-```
-pnpm version minor
-```

package/dist/AddHighlightModel/GenomeTo1DProteinHoverHighlight.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import Highlight from './Highlight';
-import { getProteinLinkage, linkageGenomeMapping } from '../Protein1DLinkage';
+import { getProteinLinkage, getProteinLinkageMapping, } from '../Protein1DLinkage';
 import { genomeHoverToTranscriptPos } from '../ProteinView/util';
 const GenomeTo1DProteinHoverHighlight = observer(function GenomeTo1DProteinHoverHighlight({ model, }) {
     const session = getSession(model);
@@ -13,7 +13,7 @@ const GenomeTo1DProteinHoverHighlight = observer(function GenomeTo1DProteinHover
     if (!assemblyName || !linkage) {
         return null;
     }
-    const proteinPos = genomeHoverToTranscriptPos(hovered, linkageGenomeMapping(linkage));
+    const proteinPos = genomeHoverToTranscriptPos(hovered, getProteinLinkageMapping(model));
     if (proteinPos === undefined) {
         return null;
     }

package/dist/AddHighlightModel/HighlightComponents.js

@@ -3,11 +3,11 @@ import { observer } from 'mobx-react';
 import GenomeMouseoverHighlight from './GenomeMouseoverHighlight';
 import GenomeTo1DProteinHoverHighlight from './GenomeTo1DProteinHoverHighlight';
 import Protein1DToGenomeHoverHighlight from './Protein1DToGenomeHoverHighlight';
-import { ProteinToGenomeClickHighlight, ProteinToGenomeHoverHighlight, } from './ProteinToGenomeHighlight';
+import ProteinToGenomeHighlight from './ProteinToGenomeHighlight';
 const HighlightComponents = observer(function Highlight({ model, }) {
     return (React.createElement(React.Fragment, null,
-        React.createElement(ProteinToGenomeClickHighlight, { model: model }),
-        React.createElement(ProteinToGenomeHoverHighlight, { model: model }),
+        React.createElement(ProteinToGenomeHighlight, { model: model, field: "clickGenomeHighlights" }),
+        React.createElement(ProteinToGenomeHighlight, { model: model, field: "hoverGenomeHighlights" }),
         React.createElement(Protein1DToGenomeHoverHighlight, { model: model }),
         React.createElement(GenomeTo1DProteinHoverHighlight, { model: model }),
         React.createElement(GenomeMouseoverHighlight, { model: model })));

package/dist/AddHighlightModel/Protein1DToGenomeHoverHighlight.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import Highlight from './Highlight';
-import { findProteinLinkedView, genomeHighlightForProteinPosition, getProteinLinkage, } from '../Protein1DLinkage';
+import { findProteinLinkedView, genomeHighlightsForProteinPosition, getProteinLinkage, getProteinLinkageMapping, } from '../Protein1DLinkage';
 import { checkHovered } from '../ProteinView/util';
 // A hover on a 1D protein-annotation view names the UniProt entry as its
 // refName; this paints the codon on the genome view that 1D view was launched
@@ -15,20 +15,13 @@ const Protein1DToGenomeHoverHighlight = observer(function Protein1DToGenomeHover
         return null;
     }
     const { coord, refName } = hovered.hoverPosition;
-    const linkage = getProteinLinkage(findProteinLinkedView(session, refName));
+    const linkedView = findProteinLinkedView(session, refName);
+    const linkage = getProteinLinkage(linkedView);
+    const mapping = getProteinLinkageMapping(linkedView);
     const assemblyName = assemblyNames[0];
-    if (linkage?.connectedViewId !== viewId || !assemblyName) {
+    if (linkage?.connectedViewId !== viewId || !mapping || !assemblyName) {
         return null;
     }
-    const genomeHighlight = genomeHighlightForProteinPosition(linkage, coord - 1);
-    if (!genomeHighlight) {
-        return null;
-    }
-    return (React.createElement(Highlight, { model: model, region: {
-            start: genomeHighlight.start,
-            end: genomeHighlight.end,
-            refName: genomeHighlight.refName,
-            assemblyName,
-        } }));
+    return (React.createElement(React.Fragment, null, genomeHighlightsForProteinPosition(mapping, coord - 1).map(r => (React.createElement(Highlight, { key: r.start, model: model, region: { ...r, assemblyName } })))));
 });
 export default Protein1DToGenomeHoverHighlight;

package/dist/AddHighlightModel/ProteinToGenomeHighlight.js

@@ -1,9 +1,24 @@
 import React from 'react';
+import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import ProteinToGenomeHighlightInner from './ProteinToGenomeHighlightInner';
-export const ProteinToGenomeClickHighlight = observer(function ProteinToGenomeClickHighlight({ model, }) {
-    return (React.createElement(ProteinToGenomeHighlightInner, { model: model, field: "clickGenomeHighlights" }));
-});
-export const ProteinToGenomeHoverHighlight = observer(function ProteinToGenomeHoverHighlight({ model, }) {
-    return (React.createElement(ProteinToGenomeHighlightInner, { model: model, field: "hoverGenomeHighlights" }));
+import Highlight from './Highlight';
+import { getProteinViews, getStructuresConnectedTo } from './proteinViewLookup';
+const ProteinToGenomeHighlight = observer(function ProteinToGenomeHighlight({ model, field, }) {
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    const { assemblyNames, id: viewId } = model;
+    const assemblyName = assemblyNames[0];
+    const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
+    // Only structures that declare this genome view as their connection: the
+    // regions are transcript coordinates on that view's assembly, so painting
+    // them into any other genome view would place a highlight at coordinates
+    // that mean nothing there.
+    const structures = getStructuresConnectedTo(getProteinViews(session), viewId);
+    return assembly && assemblyName ? (React.createElement(React.Fragment, null, structures.flatMap((structure, idx) => structure[field].map((r, idx2) => (React.createElement(Highlight, { key: `${r.refName}-${r.start}-${r.end}-${idx}-${idx2}`, model: model, region: {
+            start: r.start,
+            end: r.end,
+            refName: r.refName,
+            assemblyName,
+        } })))))) : null;
 });
+export default ProteinToGenomeHighlight;

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -28,9 +28,14 @@ const useStyles = makeStyles()({
         alignItems: 'flex-start',
     },
 });
-const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, session, view, handleClose, lookup, sideBySide, onSideBySideChange, }) {
+const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, preferredTranscriptId, session, view, handleClose, lookup, sideBySide, onSideBySideChange, }) {
     const { classes } = useStyles();
-    const state = useAlphaFoldDBSearch({ feature, view, lookup });
+    const state = useAlphaFoldDBSearch({
+        feature,
+        view,
+        lookup,
+        preferredTranscriptId,
+    });
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             state.error ? React.createElement(ErrorMessage, { error: state.error }) : null,

package/dist/LaunchProteinView/components/FoldseekSearch.js

@@ -10,7 +10,7 @@ import PartialFailureNotice from './PartialFailureNotice';
 import TranscriptSelector from './TranscriptSelector';
 import useFoldseekSearch from '../hooks/useFoldseekSearch';
 import useTranscriptIsoformSelection from '../hooks/useTranscriptIsoformSelection';
-import { DEFAULT_DATABASES } from '../services/foldseekApi';
+import { DEFAULT_DATABASES, foldseekLengthProblem, } from '../services/foldseekApi';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -28,13 +28,17 @@ const useStyles = makeStyles()({
         alignItems: 'flex-start',
     },
 });
-const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view, handleClose, }) {
+const FoldseekSearch = observer(function FoldseekSearch({ feature, preferredTranscriptId, session, view, handleClose, }) {
     const { classes } = useStyles();
     const [userEditedSequence, setUserEditedSequence] = useState();
     const [selectedDatabases, setSelectedDatabases] = useState(DEFAULT_DATABASES);
     const [show3Di, setShow3Di] = useState(false);
     const { results, cleanedAaSequence, di3Sequence, isLoading, isPredicting, error, statusMessage, predictStructure, search, cancel, reset, } = useFoldseekSearch();
-    const { transcripts, isoformSequences, isLoading: isLoadingIsoforms, error: isoformError, partialFailure: isoformPartialFailure, selectedTranscriptId: effectiveSelectedTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: selectedIsoformData, } = useTranscriptIsoformSelection({ feature, view });
+    const { transcripts, isoformSequences, isLoading: isLoadingIsoforms, error: isoformError, partialFailure: isoformPartialFailure, selectedTranscriptId: effectiveSelectedTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: selectedIsoformData, } = useTranscriptIsoformSelection({
+        feature,
+        view,
+        preferredTranscriptId,
+    });
     const cleanedSequence = selectedIsoformData
         ? stripAllStopCodons(selectedIsoformData.seq)
         : '';
@@ -53,7 +57,11 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
         invalidatePrediction();
     };
     const isBusy = isLoading || isPredicting;
-    const canSearch = sequence.trim().length > 0 && selectedDatabases.length > 0 && !isBusy;
+    const lengthProblem = foldseekLengthProblem(sequence);
+    const canSearch = sequence.trim().length > 0 &&
+        !lengthProblem &&
+        selectedDatabases.length > 0 &&
+        !isBusy;
     // One button: predicting the 3Di alphabet is a step of the search, not a
     // decision, and making the user click twice only invited a stale prediction.
     const runSearch = async () => {
@@ -75,7 +83,7 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
                 React.createElement(TextField, { label: "Protein sequence (amino acids)", multiline: true, rows: 4, value: sequence, onChange: e => {
                         setUserEditedSequence(e.target.value);
                         invalidatePrediction();
-                    }, placeholder: `MKTVRQERLKSIVRILERSKEPVSGAQLAEEL...`, disabled: isBusy, slotProps: {
+                    }, placeholder: `MKTVRQERLKSIVRILERSKEPVSGAQLAEEL...`, disabled: isBusy, error: !!lengthProblem, helperText: lengthProblem, slotProps: {
                         input: { className: classes.sequenceInput },
                     } }))) : null,
             di3Sequence ? (React.createElement("div", { className: classes.di3Section },

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js

@@ -10,7 +10,7 @@ import TabPanel from './TabPanel';
 import UserProvidedStructure from './UserProvidedStructure';
 import useUniProtIdLookup from '../hooks/useUniProtIdLookup';
 import { getLaunchSideBySide, setLaunchSideBySide } from '../utils/sideBySide';
-export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
+export default function LaunchProteinViewDialog({ handleClose, feature, preferredTranscriptId, model, }) {
     const [choice, setChoice] = useState(0);
     const session = getSession(model);
     const view = getContainingView(model);
@@ -36,11 +36,11 @@ export default function LaunchProteinViewDialog({ handleClose, feature, model, }
             React.createElement(Tab, { value: 2, label: "Foldseek search" }),
             React.createElement(Tab, { value: 3, label: "File or URL" })),
         React.createElement(TabPanel, { value: choice, index: 0 },
-            React.createElement(AlphaFoldDBSearch, { session: session, view: view, feature: feature, handleClose: handleClose, lookup: lookup, sideBySide: sideBySide, onSideBySideChange: changeSideBySide })),
+            React.createElement(AlphaFoldDBSearch, { session: session, view: view, feature: feature, preferredTranscriptId: preferredTranscriptId, handleClose: handleClose, lookup: lookup, sideBySide: sideBySide, onSideBySideChange: changeSideBySide })),
         React.createElement(TabPanel, { value: choice, index: 1 },
-            React.createElement(PdbSearch, { session: session, view: view, feature: feature, handleClose: handleClose, lookup: lookup, sideBySide: sideBySide, onSideBySideChange: changeSideBySide })),
+            React.createElement(PdbSearch, { session: session, view: view, feature: feature, preferredTranscriptId: preferredTranscriptId, handleClose: handleClose, lookup: lookup, sideBySide: sideBySide, onSideBySideChange: changeSideBySide })),
         React.createElement(TabPanel, { value: choice, index: 2 },
-            React.createElement(FoldseekSearch, { session: session, view: view, feature: feature, handleClose: handleClose })),
+            React.createElement(FoldseekSearch, { session: session, view: view, feature: feature, preferredTranscriptId: preferredTranscriptId, handleClose: handleClose })),
         React.createElement(TabPanel, { value: choice, index: 3 },
-            React.createElement(UserProvidedStructure, { session: session, view: view, feature: feature, handleClose: handleClose }))));
+            React.createElement(UserProvidedStructure, { session: session, view: view, feature: feature, preferredTranscriptId: preferredTranscriptId, handleClose: handleClose }))));
 }

package/dist/LaunchProteinView/components/PdbSearch.js

@@ -32,7 +32,7 @@ const useStyles = makeStyles()({
 // A crystal is usually a fragment, often with partners, so the view aligns
 // the transcript to it after launch rather than expecting a sequence match
 // here.
-const PdbSearch = observer(function PdbSearch({ feature, session, view, handleClose, lookup, sideBySide, onSideBySideChange, }) {
+const PdbSearch = observer(function PdbSearch({ feature, preferredTranscriptId, session, view, handleClose, lookup, sideBySide, onSideBySideChange, }) {
     const { classes } = useStyles();
     const { uniprotId, isAutoMode, isLookupLoading } = lookup;
     const { entries, error: pdbError, isLoading: isPdbLoading, } = usePdbBestStructures(uniprotId);
@@ -66,6 +66,7 @@ const PdbSearch = observer(function PdbSearch({ feature, session, view, handleCl
         feature,
         view,
         structureSequences,
+        preferredTranscriptId,
         resetKey: uniprotId,
     });
     const loadingStatuses = [

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -28,7 +28,7 @@ function HelpText() {
         React.createElement(ExternalLink, { href: "https://github.com/sokrypton/ColabFold" }, "ColabFold"),
         ". This plugin will align the protein sequence calculated from the genome to the protein sequence embedded in the structure file which allows for slight differences in these two representations."));
 }
-const UserProvidedStructure = observer(function UserProvidedStructure({ feature, session, view, handleClose, }) {
+const UserProvidedStructure = observer(function UserProvidedStructure({ feature, preferredTranscriptId, session, view, handleClose, }) {
     const { classes } = useStyles();
     const [file, setFile] = useState();
     const [choice, setChoice] = useState('file');
@@ -45,7 +45,12 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const { transcripts: options, isoformSequences, 
     // the chain the isoforms are compared against — not blindly chain 0, which
     // mismatched every heteromer the view itself went on to map correctly
-    structureSequence, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, partialFailure: isoformPartialFailure, } = useTranscriptIsoformSelection({ feature, view, structureSequences });
+    structureSequence, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, partialFailure: isoformPartialFailure, } = useTranscriptIsoformSelection({
+        feature,
+        view,
+        structureSequences,
+        preferredTranscriptId,
+    });
     const error = isoformError ?? launchError ?? fileError;
     const canLaunch = !!(activeURL || activeFile) && !!protein && !!selectedTranscript;
     const sequencesDiffer = !!protein?.seq &&

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -2,7 +2,7 @@ import { useMemo } from 'react';
 import { stripStopCodon } from 'p2s_mapper';
 import useAlphaFoldData from './useAlphaFoldData';
 import useTranscriptIsoformSelection from './useTranscriptIsoformSelection';
-export default function useAlphaFoldDBSearch({ feature, view, lookup, }) {
+export default function useAlphaFoldDBSearch({ feature, view, lookup, preferredTranscriptId, }) {
     const { uniprotId, isAutoMode, isLookupLoading } = lookup;
     const { isLoading: isAlphaFoldLoading, isValidating: isAlphaFoldValidating, error: alphaFoldError, model, noModel, } = useAlphaFoldData({ uniprotId, feature, view });
     // a stable array, or the isoform picker realigns on every render
@@ -12,6 +12,7 @@ export default function useAlphaFoldDBSearch({ feature, view, lookup, }) {
         feature,
         view,
         structureSequences,
+        preferredTranscriptId,
         resetKey: model?.url,
     });
     const loadingStatuses = [

package/dist/LaunchProteinView/hooks/useTranscriptIsoformSelection.js

@@ -8,7 +8,7 @@ import { getId, isoformRecords } from '../utils/util';
 // list transcripts, fetch their protein sequences, pick which chain of the
 // structure to compare against, auto/manually select a transcript, and resolve
 // the selection back to its feature + sequence.
-export default function useTranscriptIsoformSelection({ feature, view, structureSequences, resetKey, }) {
+export default function useTranscriptIsoformSelection({ feature, view, structureSequences, preferredTranscriptId, resetKey, }) {
     const transcripts = codingTranscripts(feature);
     const { isoformSequences, isLoading, error, partialFailure } = useIsoformProteinSequences({
         feature,
@@ -20,6 +20,7 @@ export default function useTranscriptIsoformSelection({ feature, view, structure
         options: transcripts,
         isoformSequences,
         structureSequence,
+        preferredTranscriptId,
         resetKey,
     });
     const selectedTranscript = transcripts.find(f => getId(f) === userSelection);

package/dist/LaunchProteinView/hooks/useTranscriptSelection.js

@@ -1,7 +1,17 @@
 import { useState } from 'react';
 import { selectBestTranscript } from 'p2s_mapper';
 import { rankableIsoforms } from '../utils/util';
-export default function useTranscriptSelection({ options, isoformSequences, structureSequence, resetKey, }) {
+/**
+ * The isoform the user right-clicked when it translates, else the one whose
+ * protein best matches the structure.
+ */
+export function defaultTranscriptId({ options, isoformSequences, structureSequence, preferredTranscriptId, }) {
+    const isoforms = rankableIsoforms(options, isoformSequences);
+    return isoforms.some(i => i.id === preferredTranscriptId && i.seq)
+        ? preferredTranscriptId
+        : selectBestTranscript({ isoforms, structureSequence });
+}
+export default function useTranscriptSelection({ options, isoformSequences, structureSequence, preferredTranscriptId, resetKey, }) {
     const [userSelection, setUserSelection] = useState();
     const [prevResetKey, setPrevResetKey] = useState(resetKey);
     if (resetKey !== prevResetKey) {
@@ -9,9 +19,11 @@ export default function useTranscriptSelection({ options, isoformSequences, stru
         setUserSelection(undefined);
     }
     const autoSelection = isoformSequences !== undefined
-        ? selectBestTranscript({
-            isoforms: rankableIsoforms(options, isoformSequences),
+        ? defaultTranscriptId({
+            options,
+            isoformSequences,
             structureSequence,
+            preferredTranscriptId,
         })
         : undefined;
     return { userSelection: userSelection ?? autoSelection, setUserSelection };

package/dist/LaunchProteinView/index.js

@@ -17,6 +17,7 @@ function canvasTarget(info, fetchFullFeature) {
         : {
             type,
             fetchFeature: () => fetchFullFeature(parentId, displayedRegionIndex),
+            preferredTranscriptId: subfeature?.featureId,
         };
 }
 // The hit test only carries a type, so a canvas host learns whether the gene
@@ -27,9 +28,13 @@ function legacyTarget(feature) {
     const type = root.get('type');
     return type === undefined || !isCodingFeature(root)
         ? undefined
-        : { type, feature: root };
+        : {
+            type,
+            feature: root,
+            preferredTranscriptId: root === feature ? undefined : feature.id(),
+        };
 }
-function resolveTarget(self) {
+export function resolveTarget(self) {
     const { contextMenuFeature, contextMenuInfo, fetchFullFeature } = self;
     return contextMenuInfo && fetchFullFeature
         ? canvasTarget(contextMenuInfo, fetchFullFeature)
@@ -40,10 +45,11 @@ function resolveTarget(self) {
 function launchProteinView(self, target) {
     const track = getContainingTrack(self);
     const session = getSession(track);
+    const { preferredTranscriptId } = target;
     const openDialog = (feature) => {
         session.queueDialog(handleClose => [
             LaunchProteinViewDialog,
-            { model: track, handleClose, feature },
+            { model: track, handleClose, feature, preferredTranscriptId },
         ]);
     };
     if ('feature' in target) {

package/dist/LaunchProteinView/services/foldseekApi.js

@@ -13,16 +13,27 @@ export const DEFAULT_DATABASES = [
     'pdb100',
     'afdb-swissprot',
 ];
-export async function predict3Di({ aaSequence, signal, }) {
-    // Clean the sequence - remove FASTA header, whitespace, stop codons, and non-AA chars
-    const cleanSequence = aaSequence
+export const FOLDSEEK_MAX_RESIDUES = 1200;
+export function cleanFoldseekSequence(aaSequence) {
+    return aaSequence
         .split('\n')
         .filter(line => !line.startsWith('>'))
         .join('')
-        .replace(/\s/g, '')
-        .replace(/\*/g, '') // Remove stop codons before querying 3Di
         .toUpperCase()
-        .replace(/[^ACDEFGHIKLMNPQRSTVWY]/g, ''); // Keep only valid amino acids
+        .replace(/[^ACDEFGHIKLMNPQRSTVWY]/g, '');
+}
+export function foldseekLengthProblem(aaSequence) {
+    const { length } = cleanFoldseekSequence(aaSequence);
+    return length > FOLDSEEK_MAX_RESIDUES
+        ? `Foldseek's 3Di predictor takes at most ${FOLDSEEK_MAX_RESIDUES.toLocaleString('en-US')} residues and this sequence has ${length.toLocaleString('en-US')}. Trim it to the region you want to search.`
+        : undefined;
+}
+export async function predict3Di({ aaSequence, signal, }) {
+    const problem = foldseekLengthProblem(aaSequence);
+    if (problem) {
+        throw new Error(problem);
+    }
+    const cleanSequence = cleanFoldseekSequence(aaSequence);
     const url = `https://3di.foldseek.com/predict/${encodeURIComponent(cleanSequence)}`;
     const response = await rawfetch(url, { signal });
     if (!response.ok) {

package/dist/LaunchProteinView/utils/calculateProteinSequence.js

@@ -1,18 +1,21 @@
 import { getConf } from '@jbrowse/core/configuration';
 import { revcom } from '@jbrowse/core/util';
 import { convertCodingSequenceToPeptides } from '@jbrowse/core/util/convertCodingSequenceToPeptides';
-import { getGeneticCode, parseTranslTable, } from '@jbrowse/core/util/geneticCodes';
+import { getGeneticCode, parseTranslTable, relativizeTranslExcept, } from '@jbrowse/core/util/geneticCodes';
 import { isCDS } from '../codingFeature';
-export function calculateProteinSequence({ cds, sequence, geneticCodeId, }) {
-    // `starts` is deliberately not passed: @jbrowse/core 4.3.0's signature has no
-    // such parameter, so alternative initiators (GTG under table 11, ATA under
-    // table 2) render as their internal residue rather than M. Core main added it;
-    // pass it here when the @jbrowse/core floor reaches that release.
-    const { codonTable } = getGeneticCode(geneticCodeId);
+/**
+ * The translation core's feature panel shows: the genetic code's alternative
+ * initiators read as M, and a `transl_except` (RefSeq's selenocysteines) as its
+ * named residue.
+ */
+export function calculateProteinSequence({ cds, sequence, geneticCodeId, translExcept, }) {
+    const { codonTable, starts } = getGeneticCode(geneticCodeId);
     return convertCodingSequenceToPeptides({
         cds,
         sequence,
         codonTable,
+        starts,
+        translExcept,
     });
 }
 function revlist(list, seqlen) {
@@ -51,10 +54,19 @@ export function getProteinSequence({ feature, seq, assemblyGeneticCodeId, }) {
     const geneticCodeId = parseTranslTable(feature.get('transl_table')) ??
         parseTranslTable(cdsSubfeature?.get('transl_table')) ??
         assemblyGeneticCodeId;
+    const rawTranslExcept = feature.get('transl_except') ?? cdsSubfeature?.get('transl_except');
     return calculateProteinSequence({
         cds: strand === -1 ? revlist(cds, seq.length) : cds,
         sequence: strand === -1 ? revcom(seq) : seq,
         geneticCodeId,
+        translExcept: rawTranslExcept
+            ? relativizeTranslExcept({
+                raw: rawTranslExcept,
+                featureStart,
+                featureLength: seq.length,
+                strand,
+            })
+            : undefined,
     });
 }
 /** The genome under one span, with the assembly's code for that contig. */