Coloring

Representations

stage.loadFile("rcsb://1crn").then(function (o) {
  o.addRepresentation("ball+stick", {colorScheme: "bfactor"});
  o.autoView();
});

Available schemes

• atomindex
• bfactor
• chainid
• chainindex
• chainname
• densityfit
• electrostatic
• element
• entityindex
• entitytype
• geoquality
• hydrophobicity
• modelindex
• moleculetype
• occupancy
• random
• residueindex
• resname
• sstruc
• uniform
• value
• volume

Selection-based coloring

Create and a selection-based coloring scheme. Supply a list with pairs of colorname and selection for coloring by selections. Use the last entry as a default (catch all) coloring definition.

var schemeId = NGL.ColormakerRegistry.addSelectionScheme([
  ["red", "64-74 or 134-154 or 222-254 or 310-310 or 322-326"],
  ["green", "311-322"],
  ["yellow", "40-63 or 75-95 or 112-133 or 155-173 or 202-221 or 255-277 or 289-309"],
  ["blue", "1-39 or 96-112 or 174-201 or 278-288"],
  ["white", "*"]
], "Transmembrane 3dqb");

stage.loadFile("rcsb://3dqb.pdb").then(function (o) {
  o.addRepresentation("cartoon", {color: schemeId });  // pass schemeId here
  o.autoView();
});

Custom coloring

Create a class with a atomColor method that returns a hex color:

var schemeId = NGL.ColormakerRegistry.addScheme(function (params) {
  this.atomColor = function (atom) {
    if (atom.serial < 1000) {
      return 0x0000FF;  // blue
    } else if (atom.serial > 2000) {
      return 0xFF0000;  // red
    } else {
      return 0x00FF00;  // green
    }
  };
});

stage.loadFile("rcsb://3dqb.pdb").then(function (o) {
  o.addRepresentation("cartoon", {color: schemeId});  // pass schemeId  here
  o.autoView();
});