Interactive PDB Viewing

Generate a quick NGL (webGL based) structure overview of bio3d pdb class objects with a number of simple defaults. The returned NGLVieweR object can be further added to for custom interactive visualizations.

Usage

view.pdb(
  pdb,
  cols = NULL,
  colorScheme = "residueindex",
  representation = "cartoon",
  ligand = TRUE,
  ligand.style = "licorice",
  backgroundColor = "white",
  highlight = NULL,
  highlight.style = "ball+stick",
  water.rm = FALSE
)

view.old(
  pdb,
  ligand = TRUE,
  chain.colors = bio3d::vmd_colors(),
  backgroundColor = "white",
  highlight = NULL,
  highlight.style = "ball+stick"
)

Arguments

pdb

a PDB structure object as obtained from read.pdb().

cols

a vector of colors, typically one entry per chain. If NULL then colorScheme is used. If numeric then output of vmd.colors(cols) is used.

colorScheme

keyword based coloring used only if cols input is NULL. Possible values include "residueindex", "modelindex", "sstruc", "bfactor", "chainid", "chainindex", "atomindex", and "occupancy".

representation

the representation style, useful values are "line", "tube", "cartoon", "trace", "backbone", and "ball+stick".

ligand

logical, if TRUE ligands will be rendered as atom colored ligand.style.

ligand.style

the representation style to use for ligands.

backgroundColor

a single element color vector that set the display area background color.

highlight

an optional atom.select() object for highlighting.

highlight.style

the representation style to use for selected highlight atoms.

water.rm

logical, if TRUE water molecules are removed pior to viewing.

chain.colors

Color vector parameter specific to coloring by chain

Value

an NGLVieweR display object that can be displayed or further added to using NGLVieweR::addRepresentation() and friends.

Details

The purpose of this function is to quickly view a given PDB structure object without having to write output files for input to molecular graphics programs or write multiple lines of NGLVieweR code.

The extra argument highlight takes a bio3d atom.select() object to highlight atom subsets as a given highlight.style. Useful highlight.style options include: "ball+stick", "spacefill", "licorice", "line", "surface" and "ribbon".

The full set of supported representation styles include:

• "cartoon",

• "ribbon",

• "tube",

• "trace",

• "ball+stick",

• "line",

• "backbone",

• "licorice",

• "surface",

• "point",

• "rope",

• "spacefill".

Available colorScheme options include:

• "residueindex",

• "resname",

• "modelindex",

• "sstruc",

• "bfactor",

• "chainid",

• "chainindex",

• "chainname",

• "atomindex",

• "occupancy",

• "hydrophobicity",

• "random",

• "element",

• "validation",

Limitations: Currently the function attempts to map common abbreviations and acronyms of colorScheme and representation values (e.g. "cpk" for "ballandstick", "sse" for "sstruct", etc.). If a mapping is not available then the default values of "residueindex" and "ball+stick" are used respectively. Currently the function does not check for bio3d or NGLVieweR availability. It also does not work well with trajectory or pdbs objects. For the later use view.pdbs().

Functions

• view.old(): An alternative pdb viewer function

See also

pdb2string(), view.pdbs(), NGLVieweR::NGLVieweR(), bio3d::read.pdb()

Author

Barry Grant, bjgrant@ucsd.edu

Examples

 pdb <- bio3d::read.pdb("1hsg")
#>   Note: Accessing on-line PDB file
#> Warning: /var/folders/jd/wjwf0lcj0kd0tch_70sd1l4w0000gn/T//RtmpEoJQ6k/1hsg.pdb  exists. Skipping download
 view.pdb(pdb)

 view.pdb(pdb, ligand=FALSE, cols=c("pink","aquamarine"))
#> Potential ligands found but not displayed, use ligand=T to view

 view.pdb(pdb, colorScheme = "sstruc")


 #ras <- read.pdb("5p21")
 #view.pdb(ras)

 sele <- bio3d::atom.select(pdb, resno=c(25, 50))
 view.pdb(pdb, highlight = sele,
        cols = c("navy","orange"),
        backgroundColor = "pink",
        highlight.style = "spacefill")