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index.html
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978 lines (953 loc) · 39.8 KB
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<link rel="icon" href="./favicon.ico" type="image/x-icon">
<title>RCSB PDB Mol* Viewer</title>
<style>
* {
margin: 0;
padding: 0;
box-sizing: border-box;
}
#viewer {
position: absolute;
left: 5%;
top: 100px;
min-width: 90%;
height: 85%;
}
.msp-layout-expanded {
z-index: 10;
}
#menu {
position: absolute;
left: 5%;
top: 20px;
}
#menu > select {
width: 200px;
}
</style>
<link rel="stylesheet" type="text/css" href="rcsb-molstar.css" />
<script type="text/javascript" src="./rcsb-molstar.js"></script>
</head>
<body>
<div id="viewer"></div>
<script>
function getQueryParam(id) {
const a = new RegExp(id + '=([^&#=]*)', 'i')
const m = a.exec(window.location.search)
return m ? decodeURIComponent(m[1]) : undefined
}
const isEmbedded = getQueryParam('embedded') === '1';
const pdbId = getQueryParam('pdbId')
const url = getQueryParam('url')
const _config = getQueryParam('config')
const config = _config && JSON.parse(_config)
const _loadPdbIds = getQueryParam('loadPdbIds')
const loadPdbIds = _loadPdbIds && JSON.parse(_loadPdbIds)
// create an instance of the plugin
const viewer = new rcsbMolstar.Viewer('viewer', {
showImportControls: !pdbId,
showSessionControls: !pdbId,
layoutShowLog: !pdbId,
layoutShowControls: !isEmbedded,
showMembraneOrientationPreset: true,
showNakbColorTheme: true,
detachedFromSierra: true, // needed when running without sierra
pickingAlphaThreshold: 0.2,
manualReset: true
})
// load pdbId or url
if (pdbId) viewer.loadPdbId(pdbId, config)
else if (loadPdbIds) viewer.loadPdbIds(loadPdbIds);
else if (url) viewer.loadStructureFromUrl(url, config)
</script>
<div id="menu">
<h2> RCSB PDB Mol* Viewer - Test Page</h2>
<label for="examples">Examples</label>
<select id="examples" onchange="loadExample(parseInt(this.value))">
<option value=''></option>
</select>
Clear
<button style="padding: 3px;" onclick="viewer.clear()">all</button>
<button style="padding: 3px;" onclick="superposed()">Superposed</button>
<button style="padding: 3px;" onclick="motifs1()">Motifs 1</button>
<button style="padding: 3px;" onclick="motifs2()">Motifs 2</button>
<button style="padding: 3px;" onclick="motifsAlphaFold()">Motifs AF</button>
<button style="padding: 3px" onclick="alignment()">Alignment</button>
</div>
<script>
function loadExample(index) {
const e = examples[index];
// let URL, if specified, take precedence over ID
if (e.url) {
return viewer.loadStructureFromUrl(e.url, e.format ?? 'mmcif', e.isBinary ?? false, e.config).then(_ => viewer.resetCamera(0))
}
if (e.id) {
return viewer.loadPdbId(e.id, e.config).then(_ => viewer.resetCamera(0))
}
}
const examples = [
{
id: '1CRN',
info: 'small: only polymer',
config: {
props: {
kind: 'validation'
}
}
},
{
id: '3CUP',
info: 'small',
config: {
props: {
kind: 'density'
}
}
},
{
id: '3PQR',
info: 'medium: polymer, carbs, ligands',
config: {
props: {
kind: 'feature',
assemblyId: '2',
target: {
labelCompId: 'RET'
}
}
}
},
{
id: '1NMR',
info: 'medium: nmr models',
config: {
props: {
kind: 'standard',
modelIndex: 2
}
}
},
{
id: '4HHB',
info: 'medium: classic, lots of validation geometry problems',
config: {
props: {
kind: 'standard',
assemblyId: '1'
}
}
},
{
id: '1A6D',
info: 'medium: dihedral symmetry (D8)',
config: {
props: {
kind: 'symmetry',
assemblyId: '1',
symmetryIndex: 1
}
}
},
{
id: '1LTI',
info: 'medium: local symmetry (C5)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '1QO1',
info: 'medium: C-alpha only, local symmetries (C10, C3)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6V9Q',
info: 'medium: local symmetries (H, C2)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6R6B',
info: 'medium: local symmetries (H x2)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '2VTU',
info: 'medium: octahedral symmetry (O)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '4NWP',
info: 'medium: tetrahedral symmetry (T)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '1RB8',
info: 'medium-large: small virus capsid, icosahedral symmetry (I)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6QVK',
info: 'large: The cryo-EM structure of bacteriophage phi29 prohead (C5)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5Y6P',
info: 'large: Structure of the phycobilisome from the red alga Griffithsia pacifica',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6O2S',
info: 'large: Deacetylated Microtubules (H)',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5MQ7',
info: 'large: Structure of AaLS-13',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5IV5',
info: 'large: Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '3JC8',
info: 'large: Architectural model of the type IVa pilus machine in a piliated state',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '4V99',
info: 'large: The Crystallographic Structure of Panicum Mosaic Virus',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '3J3Q',
info: 'large: Atomic-level structure of the entire HIV-1 capsid',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6NCL',
info: 'large: Near-atomic structure of icosahedrally averaged PBCV-1 capsid',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6EKC',
info: 'large: Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus',
props: {
assemblyId: '1'
}
},
{
id: '1M4X',
info: 'large: PBCV-1 virus capsid, quasi-atomic model',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '4V5A',
info: 'large: Structure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMet',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '4UDF',
info: 'large: STRUCTURAL BASIS OF HUMAN PARECHOVIRUS NEUTRALIZATION BY HUMAN MONOCLONAL ANTIBODIES',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6J5K',
info: 'Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6RVV',
info: 'Structure of left-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6EK5',
info: 'Near-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '4V93',
info: 'Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5VLZ',
info: 'Backbone model for phage Qbeta capsid',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5XTI',
info: 'Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6BY7',
info: 'Folding DNA into a lipid-conjugated nano-barrel for controlled reconstitution of membrane proteins',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6C50',
info: 'Cross-alpha Amyloid-like Structure alphaAmS',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '6K3I',
info: 'Salmonella hook in curved state - 66 subunit models',
props: {
assemblyId: '1'
}
},
{
id: '1UNO',
info: 'Crystal structure of a d,l-alternating peptide. Double-starnded helix from beta-sheets.',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '1GRM',
info: 'REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL. Single-starnded helix from beta-sheet. NMR structure.',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '1B5F',
info: 'oligosaccharide: NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.',
config: {
props: {
kind: 'feature',
target: {
labelAsymId: 'E',
extendToChain: true
}
}
}
},
{
id: '1BCS',
// this should focus on 1 of 2 (!) ARGs in chain G
info: 'ligand: COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, CHYMOSTATIN, AND ARGININE AT 100 DEGREES KELVIN\n',
config: {
props: {
kind: 'feature',
assemblyId: '1',
target: {
labelAsymId: 'F'
}
}
}
},
{
id: '1BRR',
info: 'membrane: X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX with ANVIL membrane prediction',
config: {
props: {
kind: 'membrane'
}
}
},
{
id: '3SN6',
info: 'membrane: Crystal structure of the beta2 adrenergic receptor-Gs protein complex with ANVIL membrane prediction',
config: {
props: {
kind: 'membrane'
}
}
},
{
id: '1SQX',
info: 'membrane + assembly: Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A',
config: {
props: {
kind: 'membrane',
assemblyId: '1'
}
}
},
{
id: '5XES',
// this will fail membrane calculation due to tiny size but should still show default representation
info: 'failing membrane: TK9 NMR structure in SDS micelle',
config: {
props: {
kind: 'membrane',
assemblyId: '1'
}
}
},
{
id: '6WJC',
info: 'ligand validation: Muscarinic acetylcholine receptor 1 - muscarinic toxin 7 complex: Focus + Density',
config: {
props: {
kind: 'feature-density',
target: {
labelAsymId: 'D',
authSeqId: 502
},
radius: 0,
hiddenChannels: ['fo-fc(+ve)', 'fo-fc(-ve)']
}
}
},
{
id: '5RL9',
info: 'ligand focus on wrong assembly: Crystal Structure of SARS-CoV-2 helicase in complex with Z1703168683',
config: {
props: {
kind: 'feature',
assemblyId: '1',
// UR7 is not present in assembly 1
target: {
labelCompId: 'UR7'
}
}
}
},
{
id: '5VL5',
info: 'motif selection with operator: Coordination Chemistry within a Protein Host: Regulation of the Secondary Coordination Sphere',
config: {
props: {
kind: 'motif',
assemblyId: '1',
targets: [
{ labelAsymId: 'A', labelSeqId: 61, operatorName: 'ASM_1' },
{ labelAsymId: 'A', labelSeqId: 69, operatorName: 'ASM_1' },
{ labelAsymId: 'A', labelSeqId: 87, operatorName: 'ASM_4' }
],
}
}
},
{
id: '5VL5',
info: 'motif selection with strucmotif-expression: Coordination Chemistry within a Protein Host: Regulation of the Secondary Coordination Sphere',
config: {
props: {
kind: 'motif',
assemblyId: '1',
targets: [
{ labelAsymId: 'A', labelSeqId: 61, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 69, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 87, structOperId: '4' }
],
}
}
},
{
id: '2BFU',
info: 'motif selection with strucmotif-expression: X-ray structure of CPMV top component',
config: {
props: {
kind: 'motif',
assemblyId: '6',
targets: [
{ labelAsymId: 'A', labelSeqId: 46, structOperId: 'X0x5' },
{ labelAsymId: 'A', labelSeqId: 49, structOperId: 'X0x5' },
{ labelAsymId: 'A', labelSeqId: 145, structOperId: 'X0x5' }
],
}
}
},
{
id: '1G2F',
info: 'motif selection with strucmotif-expression & chain: STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6)',
config: {
props: {
kind: 'motif',
targets: [
{ labelAsymId: 'F', labelSeqId: 7 },
{ labelAsymId: 'F', labelSeqId: 25 },
{ labelAsymId: 'F', labelSeqId: 29 }
],
}
}
},
{
id: '3IDH',
info: 'motif + carbo: Human pancreatic glucokinase in complex with glucose',
config: {
props: {
kind: 'motif',
assemblyId: '1',
targets: [
{ labelAsymId: 'A', labelSeqId: 174 },
{ labelAsymId: 'A', labelSeqId: 210 }
],
}
}
},
{
id: '9A8B',
info: 'motif + IHM: Dipeptide repeat designed model, 4x DPR2, verified with CD and NMR data',
config: {
props: {
kind: 'motif',
label: '9A8B',
targets: [
{ labelAsymId: 'A', structOperId: '1', labelSeqId: 3 },
{ labelAsymId: 'A', structOperId: '1', labelSeqId: 5 },
{ labelAsymId: 'A', structOperId: '1', labelSeqId: 7 },
{ labelAsymId: 'A', structOperId: '1', labelSeqId: 9 },
],
}
}
},
{
id: 'AF-Q8W3K0-F1',
url: 'https://alphafold.ebi.ac.uk/files/AF-Q8W3K0-F1-model_v4.cif',
info: 'pLDDT coloring (external): Probable disease resistance protein At1g58602'
},
{
id: 'ma-bak-cepc-0003',
url: 'https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0003.cif',
info: 'pLDDT coloring (external): Predicted interaction between Ribosome biogenesis protein ERB1 (Eukaryotic ribosome biogenesis protein 1) and Ribosome biogenesis protein BRX1'
},
{
id: 'AF_AFQ5VSL9F1',
info: 'pLDDT coloring (internal): Striatin-interacting protein 1'
},
{
id: '7N5D',
info: 'EM: Composite Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN',
config: {
props: {
kind: 'density'
}
}
},
{
id: '5MRX',
info: 'NAKB: RNA sarcin-ricin loop',
config: {
props: {
kind: 'nakb'
}
}
},
{
id: '1G2F',
info: 'NAKB: structure of a Cys2His2 zinc finger/TATA box complex',
config: {
props: {
kind: 'nakb'
}
}
},
{
id: '1DTJ',
info: 'RSCC: CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN',
config: {
props: {
assemblyId: '1'
}
}
},
{
id: '5UJC',
info: 'Ligand wireframe: Crystal structure of a C.elegans B12-trafficking protein CblC, a human MMACHC homologue',
config: {
props: {
kind: 'feature-density',
radius: 5,
hiddenChannels: [],
wireframe: true,
target: {
labelAsymId: 'B'
}
}
}
},
{
id: '7XIW',
info: 'Glyco: SARS-CoV-2 Omicron BA.2 variant spike (state 1)',
config: {
props: {
kind: 'glygen',
focus: {
labelAsymId: 'B'
},
glycosylation: [
{
labelAsymId: 'I' // oligo interactions
}, {
labelAsymId: 'J'
}, {
labelAsymId: 'K'
}, {
labelAsymId: 'L'
}, {
labelAsymId: 'M'
}, {
labelAsymId: 'Z' // monosaccharide interactions
}, {
labelAsymId: 'AA'
}, {
labelAsymId: 'BA'
}, {
labelAsymId: 'DA'
}, {
labelAsymId: 'EA'
}, {
labelAsymId: 'FA'
}, {
labelAsymId: 'GA'
}, {
labelAsymId: 'HA'
}, {
labelAsymId: 'IA'
}
]
}
}
}
];
const examplesSelect = document.getElementById('examples');
for (let i = 0, il = examples.length; i < il; ++i) {
const e = examples[i]
const option = document.createElement('option')
Object.assign(option, { text: '[' + e.id + '] ' + e.info, value: i })
examplesSelect.appendChild(option)
}
//
function superposed() {
viewer.clear()
.then(function() {
return viewer.loadPdbId('3pqr', { props: { kind: 'standard', assemblyId: '1' } })
})
.then(function() {
return viewer.loadPdbId('1u19', { props: { kind: 'standard', assemblyId: '1' }, matrix: [
-0.67160917400372, 0.28222298510688404, 0.6850488398834855, 0,
0.13262098666685063, 0.9554691407700946, -0.26361033961856695, 0,
-0.7289399153866256, -0.08619120567473626, -0.6791305379047228, 0,
-7.602670654900173, -30.317901981509067, 24.605855585357773, 1
] })
})
.then(function() {
viewer.resetCamera(0)
});
}
function motifs1() {
viewer.clear()
.then(function() {
return viewer.loadPdbIds([
{
pdbId: '4CHA',
config: {
props: {
kind: 'motif',
label: '4CHA',
targets: [
{ labelAsymId: 'B', structOperId: '1', labelSeqId: 42 },
{ labelAsymId: 'B', structOperId: '1', labelSeqId: 87 },
{ labelAsymId: 'C', structOperId: '1', labelSeqId: 47 }
]
}
}
}, {
pdbId: '3RU4',
config: {
props: {
kind: 'motif',
assemblyId: '1',
label: '3RU4 #2: 0.26 Å',
targets: [
{ labelAsymId: 'D', structOperId: '2', labelSeqId: 42 },
{ labelAsymId: 'D', structOperId: '2', labelSeqId: 87 },
{ labelAsymId: 'E', structOperId: '2', labelSeqId: 46 }
]
},
matrix: [
-0.049396686, -0.99700946, -0.059431925, 0.0,
-0.7568329, 0.076193266, -0.6491522, 0.0,
0.6517392, 0.012914069, -0.7583332, 0.0,
20.371853, 11.498471, 45.705563, 1.0
]
}
}
]);
});
}
function motifs2() {
viewer.clear()
.then(function() {
return viewer.loadPdbIds([{
pdbId: '1M4X',
config: {
props: {
label: '1M4X',
kind: 'motif',
// assemblyId: '7', // library should be able to infer assemblyId of the query
targets: [
{ labelAsymId: 'C', labelSeqId: 161, structOperId: 'Px81' },
{ labelAsymId: 'C', labelSeqId: 165, structOperId: 'Px81' },
{ labelAsymId: 'C', labelSeqId: 170, structOperId: 'Px81' }
],
// color: 13203230
}
}
}, {
pdbId: '6KIN',
config: {
props: {
label: '6KIN @ 1.88 RMSD',
kind: 'motif',
assemblyId: '1',
targets: [
{ labelAsymId: 'B', labelSeqId: 160 },
{ labelAsymId: 'B', labelSeqId: 163 },
{ labelAsymId: 'B', labelSeqId: 167 }
],
// color: 13203230
},
matrix: [
-0.8175763932146345, -0.5719837107806522, 0.0663586909134339, 0,
-0.4927708198934652, 0.7546183669143351, 0.43327593907008527, 0,
-0.29790226638894773, 0.32153655300313416, -0.8988150448024284, 0,
340.5134831570596, -107.81055538151446, 774.3972821273203, 1.0
]
}
}]);
});
}
function motifsAlphaFold() {
viewer.clear()
.then(function() {
return viewer.loadPdbId('1LAP', {
props: {
label: '1LAP',
kind: 'motif',
targets: [
{ labelAsymId: 'A', labelSeqId: 332, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 334, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 255, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 273, structOperId: '1' },
{ labelAsymId: 'A', labelSeqId: 250, structOperId: '1' }
],
}
});
})
.then(function() {
const url = 'https://models.rcsb.org/af_aff1q6s1f1.bcif';
const label = 'AF_AFF1Q6S1F1 @ 0.23 RMSD';
const targets = [
// AF target must be devoid of struct_oper_id
{ labelAsymId: 'A', labelSeqId: 260 },
{ labelAsymId: 'A', labelSeqId: 265 },
{ labelAsymId: 'A', labelSeqId: 283 },
{ labelAsymId: 'A', labelSeqId: 342 },
{ labelAsymId: 'A', labelSeqId: 344 }
];
const matrix = [-0.471, 0.856, 0.215, 0, 0.405, -0.007, 0.914, 0, 0.784, 0.518, -0.343, 0, 54.981, 65.575, 12.287, 1];
return viewer.loadStructureFromUrl(url, 'mmcif', true, { props: { kind: 'motif', label, targets }, matrix });
});
}
function alignment() {
viewer.clear()
.then(function () {
return viewer.loadPdbIds([{
pdbId: '4HHB',
config: {
props: {
kind: 'alignment',
colors: [{
targets: [{
labelAsymId: 'A',
labelSeqRange: { beg: 4, end: 141 }
}],
value: 13203230
}],
targets: [{
labelAsymId: 'A',
labelSeqRange: { beg: 4, end: 141 }
}]
}
}
}, {
pdbId: '1OJ6',
config: {
props: {
kind: 'alignment',
colors: [{
targets: [{
labelAsymId: 'A',
labelSeqRange: { beg: 3, end: 44 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 48, end: 49 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 54, end: 95 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 98, end: 149 }
}],
value: 4947916
}],
targets: [{
labelAsymId: 'A',
labelSeqRange: { beg: 3, end: 44 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 48, end: 49 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 54, end: 95 }
}, {
labelAsymId: 'A',
labelSeqRange: { beg: 98, end: 149 }
}]
},
matrix: [
-0.7236020813550785,
-0.3321785910455749,
-0.6050267857785929,
0,
0.35577249097276376,
0.5716506226719034,
-0.7393520813968539,
0,
0.591460871508533,
-0.7502485916346675,
-0.2954675755892089,
0,
-12.537202230256351,
46.79163586574549,
94.5047139772708,
1
]
}
}]);
})
.then(function () {
viewer.resetCamera(0)
});
}
</script>
</body>
</html>