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CSS

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HTML 

              
                <div id="viewport" style="width:100%; height:100%;"></div>
!

CSS 

              
                html, body { width: 100%; height: 100%; overflow: hidden; margin: 0; padding: 0; }
!

JS 

              
                // Setup to load data from rawgit
NGL.DatasourceRegistry.add(
  "data", new NGL.StaticDatasource( "//cdn.rawgit.com/arose/ngl/v0.10.5-22/data/" )
);

var edmapUrl = 'https://edmaps.rcsb.org/maps/'

// Create NGL Stage object
var stage = new NGL.Stage( "viewport" );

// Handle window resizing
window.addEventListener( "resize", function( event ){
    stage.handleResize();
}, false );


// Code for example: interactive/xray-viewer

stage.setParameters({
  cameraType: 'orthographic',
  mousePreset: 'coot'
})

function addElement (el) {
  Object.assign(el.style, {
    position: 'absolute',
    zIndex: 10
  })
  stage.viewer.container.appendChild(el)
}

function createElement (name, properties, style) {
  var el = document.createElement(name)
  Object.assign(el, properties)
  Object.assign(el.style, style)
  return el
}

function createSelect (options, properties, style) {
  var select = createElement('select', properties, style)
  options.forEach(function (d) {
    select.add(createElement('option', {
      value: d[ 0 ], text: d[ 1 ]
    }))
  })
  return select
}

function createFileButton (label, properties, style) {
  var input = createElement('input', Object.assign({
    type: 'file'
  }, properties), { display: 'none' })
  addElement(input)
  var button = createElement('input', {
    value: label,
    type: 'button',
    onclick: function () { input.click() }
  }, style)
  return button
}

var struc
function loadStructure (input) {
  struc = undefined
  surf2fofc = undefined
  surfFofc = undefined
  surfFofcNeg = undefined
  file2fofcText.innerText = '2fofc file: none'
  fileFofcText.innerText = 'fofc file: none'
  isolevel2fofcText.innerText = ''
  isolevelFofcText.innerText = ''
  boxSizeRange.value = 10
  seleInput.value = ''
  stage.setFocus(0)
  stage.removeAllComponents()
  return stage.loadFile(input).then(function (o) {
    fileStructureText.innerText = 'structure file: ' + o.name
    struc = o
    o.autoView()
    o.addRepresentation('line', {
      colorValue: 'yellow',
      linewidth: 5
    })
    o.addRepresentation('point', {
      colorValue: 'yellow',
      sizeAttenuation: false,
      pointSize: 5,
      alphaTest: 1,
      useTexture: true
    })
  })
}

var surf2fofc
function load2fofc (input) {
  return stage.loadFile(input).then(function (o) {
    file2fofcText.innerText = '2fofc file: ' + o.name
    isolevel2fofcText.innerText = '2fofc level: 1.5\u03C3'
    boxSizeRange.value = 10
    if (surfFofc) {
      isolevelFofcText.innerText = 'fofc level: 3.0\u03C3'
      surfFofc.setParameters({ isolevel: 3, boxSize: 10 })
      surfFofcNeg.setParameters({ isolevel: 3, boxSize: 10 })
    }
    surf2fofc = o.addRepresentation('surface', {
      color: 'skyblue',
      isolevel: 1.5,
      boxSize: 10,
      useWorker: false,
      contour: true,
      opaqueBack: false
    })
  })
}

var surfFofc, surfFofcNeg
function loadFofc (input) {
  return stage.loadFile(input).then(function (o) {
    fileFofcText.innerText = 'fofc file: ' + o.name
    isolevelFofcText.innerText = 'fofc level: 3.0\u03C3'
    boxSizeRange.value = 10
    if (surf2fofc) {
      isolevel2fofcText.innerText = '2fofc level: 1.5\u03C3'
      surf2fofc.setParameters({ isolevel: 1.5, boxSize: 10 })
    }
    surfFofc = o.addRepresentation('surface', {
      color: 'lightgreen',
      isolevel: 3,
      boxSize: 10,
      useWorker: false,
      contour: true,
      opaqueBack: false
    })
    surfFofcNeg = o.addRepresentation('surface', {
      color: 'tomato',
      isolevel: 3,
      negateIsolevel: true,
      boxSize: 10,
      useWorker: false,
      contour: true,
      opaqueBack: false
    })
  })
}

var loadStructureButton = createFileButton('load structure', {
  accept: '.pdb,.cif,.ent,.gz',
  onchange: function (e) {
    if (e.target.files[ 0 ]) {
      exampleSelect.value = ''
      loadStructure(e.target.files[ 0 ])
    }
  }
}, { top: '12px', left: '12px' })
addElement(loadStructureButton)

var load2fofcButton = createFileButton('load 2fofc', {
  accept: '.map,.ccp4,.brix,.dsn6,.mrc,.gz',
  onchange: function (e) {
    if (e.target.files[ 0 ]) {
      load2fofc(e.target.files[ 0 ])
    }
  }
}, { top: '36px', left: '12px' })
addElement(load2fofcButton)

var loadFofcButton = createFileButton('load fofc', {
  accept: '.map,.ccp4,.brix,.dsn6,.mrc,.gz',
  onchange: function (e) {
    if (e.target.files[ 0 ]) {
      loadFofc(e.target.files[ 0 ])
    }
  }
}, { top: '60px', left: '12px' })
addElement(loadFofcButton)

var exampleSelect = createSelect([
    [ '', 'load example' ],
    [ '3ek3', '3ek3' ],
    [ '3nzd', '3nzd' ],
    [ '1lee', '1lee' ]
], {
  onchange: function (e) {
    var id = e.target.value
    loadExample(id).then(function () {
      if (id === '3nzd') {
        seleInput.value = 'NDP'
      } else if (id === '1lee') {
        seleInput.value = 'R36 and (.C28 or .N1)'
      }
      applySele(seleInput.value)
    })
  }
}, { top: '84px', left: '12px' })
addElement(exampleSelect)

var seleText = createElement('span', {
  innerText: 'center selection',
  title: 'press enter to apply and center'
}, { top: '114px', left: '12px', color: 'lightgrey' })
addElement(seleText)

var lastSele
function checkSele (str) {
  var selection = new NGL.Selection(str)
  return !selection.selection[ 'error' ]
}
function applySele (value) {
  if (value) {
    lastSele = value
    struc.autoView(value)
    var z = stage.viewer.camera.position.z
    stage.setFocus(100 - Math.abs(z / 10))
  }
}
var seleInput = createElement('input', {
  type: 'text',
  title: 'press enter to apply and center',
  onkeypress: function (e) {
    var value = e.target.value
    var character = String.fromCharCode(e.which)
    if (e.keyCode === 13) {
      e.preventDefault()
      if (checkSele(value)) {
        if (struc) {
          applySele(value)
        }
        e.target.style.backgroundColor = 'white'
      } else {
        e.target.style.backgroundColor = 'tomato'
      }
    } else if (lastSele !== value + character) {
      e.target.style.backgroundColor = 'skyblue'
    } else {
      e.target.style.backgroundColor = 'white'
    }
  }
}, { top: '134px', left: '12px', width: '120px' })
addElement(seleInput)

var surfaceSelect = createSelect([
    [ 'contour', 'contour' ],
    [ 'wireframe', 'wireframe' ],
    [ 'smooth', 'smooth' ],
    [ 'flat', 'flat' ]
], {
  onchange: function (e) {
    var v = e.target.value
    var p
    if (v === 'contour') {
      p = {
        contour: true,
        flatShaded: false,
        opacity: 1,
        metalness: 0,
        wireframe: false
      }
    } else if (v === 'wireframe') {
      p = {
        contour: false,
        flatShaded: false,
        opacity: 1,
        metalness: 0,
        wireframe: true
      }
    } else if (v === 'smooth') {
      p = {
        contour: false,
        flatShaded: false,
        opacity: 0.5,
        metalness: 0,
        wireframe: false
      }
    } else if (v === 'flat') {
      p = {
        contour: false,
        flatShaded: true,
        opacity: 0.5,
        metalness: 0.2,
        wireframe: false
      }
    }
    stage.getRepresentationsByName('surface').setParameters(p)
  }
}, { top: '170px', left: '12px' })
addElement(surfaceSelect)

var toggle2fofcButton = createElement('input', {
  type: 'button',
  value: 'toggle 2fofc',
  onclick: function (e) {
    surf2fofc.toggleVisibility()
  }
}, { top: '194px', left: '12px' })
addElement(toggle2fofcButton)

var toggleFofcButton = createElement('input', {
  type: 'button',
  value: 'toggle fofc',
  onclick: function (e) {
    surfFofc.toggleVisibility()
    surfFofcNeg.toggleVisibility()
  }
}, { top: '218px', left: '12px' })
addElement(toggleFofcButton)

addElement(createElement('span', {
  innerText: 'box size'
}, { top: '242px', left: '12px', color: 'lightgrey' }))
var boxSizeRange = createElement('input', {
  type: 'range',
  value: 10,
  min: 1,
  max: 50,
  step: 1,
  oninput: function (e) {
    stage.getRepresentationsByName('surface').setParameters({
      boxSize: parseInt(e.target.value)
    })
  }
}, { top: '258px', left: '12px' })
addElement(boxSizeRange)

var screenshotButton = createElement('input', {
  type: 'button',
  value: 'screenshot',
  onclick: function () {
    stage.makeImage({
      factor: 1,
      antialias: false,
      trim: false,
      transparent: false
    }).then(function (blob) {
      NGL.download(blob, 'ngl-xray-viewer-screenshot.png')
    })
  }
}, { top: '282px', left: '12px' })
addElement(screenshotButton)

var loadEdmapText = createElement('span', {
  innerText: 'load edmap',
  title: 'press enter to load'
}, { top: '312px', left: '12px', color: 'lightgrey' })
addElement(loadEdmapText)

var loadEdmapInput = createElement('input', {
  type: 'text',
  title: 'press enter to load',
  onkeypress: function (e) {
    var value = e.target.value
    var character = String.fromCharCode(e.which)
    if (e.keyCode === 13) {
      e.preventDefault()
      loadStructure('rcsb://' + value)
      load2fofc(edmapUrl + value + '_2fofc.dsn6')
      loadFofc(edmapUrl + value + '_fofc.dsn6')
    }
  }
}, { top: '332px', left: '12px', width: '120px' })
addElement(loadEdmapInput)

var isolevel2fofcText = createElement(
    'span', {}, { bottom: '32px', left: '12px', color: 'lightgrey' }
)
addElement(isolevel2fofcText)

var isolevelFofcText = createElement(
    'span', {}, { bottom: '12px', left: '12px', color: 'lightgrey' }
)
addElement(isolevelFofcText)

var fileStructureText = createElement('span', {
  innerText: 'structure file: none'
}, { bottom: '52px', right: '12px', color: 'lightgrey' })
addElement(fileStructureText)

var file2fofcText = createElement('span', {
  innerText: '2fofc file: none'
}, { bottom: '32px', right: '12px', color: 'lightgrey' })
addElement(file2fofcText)

var fileFofcText = createElement('span', {
  innerText: 'fofc file: none'
}, { bottom: '12px', right: '12px', color: 'lightgrey' })
addElement(fileFofcText)

stage.mouseControls.add('scroll', function () {
  if (surf2fofc) {
    var level2fofc = surf2fofc.getParameters().isolevel.toFixed(1)
    isolevel2fofcText.innerText = '2fofc level: ' + level2fofc + '\u03C3'
  }
  if (surfFofc) {
    var levelFofc = surfFofc.getParameters().isolevel.toFixed(1)
    isolevelFofcText.innerText = 'fofc level: ' + levelFofc + '\u03C3'
  }
})

function loadExample (id) {
  var pl
  if (id === '3ek3') {
    pl = [
      loadStructure('data://3ek3.cif'),
      load2fofc('data://3ek3-2fofc.map.gz'),
      loadFofc('data://3ek3-fofc.map.gz')
    ]
  } else if (id === '3nzd') {
    pl = [
      loadStructure('data://3nzd.cif'),
      load2fofc('data://3nzd.ccp4.gz'),
      loadFofc('data://3nzd_diff.ccp4.gz')
    ]
  } else if (id === '1lee') {
    pl = [
      loadStructure('data://1lee.pdb'),
      load2fofc('data://1lee.ccp4'),
      loadFofc('data://1lee_diff.ccp4')
    ]
  }
  exampleSelect.value = ''
  return Promise.all(pl)
}

loadExample('3ek3')
!
999px

Console