Archive Trac docs ngl

Docs Ngl

Legacy Trac archive page imported from docs_ngl. Source: https://genapp.rocks/wiki/wiki/docs_ngl. Active canonical page: Reference-NGL. Review age, links, and examples before treating as current.

NGL molecular viewer

• requires genappalpha rev XXXX

• NGL provides a WebGL based molecular viewer

• examples

  • 
  • module json (note height & width must be specified, else the viewer will have no size):

     ...
     ,{
            "role"            : "output"
            ,"id"              : "nglplot"
            ,"label"           : "Example NGL"
            ,"type"            : "ngl"
            ,"height"          : "500px"
            ,"width"           : "600px"
      }
      ...

• executable JSON output

{
    "loadname"    : "myfile.pdb"
    ,"loadparams" : {
                       "ext" : "pdb"
                       ,"name" : "a name"
                       ,"asTrajectory" : true
                    }
    ,"representation" : "cartoon"

}

• notes:
  • Required:
  • "loadname" is passed to stage.loadFile()
  • Optional:
  • "loadparams" is passed as the 2nd argument to stage.loadFile()
    • "loadparams" : "ext" is an optional file extension to determine file type (if not specified in "loadname").
    • "loadparams" : "name" is an optional name for the data
    • "loadparams" : "asTrajectory" is optional, but required for multimodel PDB's to be used as trajectories
  • "representation" is an optional startup representation
    • default "cartoon"
    • possibilities:

    backbone
    ball+stick
    cartoon
    contact
    helixorient
    hyperball
    label
    licorice
    line
    point
    ribbon
    rocket
    rope
    spacefill
    surface
    trace
    tube

• TO DO:
  • add trajectory controls