Quick interactive PDBS object viewing using NGLVieweR

Please use view.pdbs() instead.

Usage

view.pdbs2(
  pdbs,
  colors = NULL,
  representation = "line",
  backgroundColor = "white"
)

Arguments

pdbs

a multi-structure pdbs object as obtained from pdbaln(), read.fasta.pdb(), etc.

colors

a vector of colors for each structure. If NULL then the output of vmd.colors() is used.

representation

the representation style, usefull values are lines, tube and cartoon.

backgroundColor

set the display area background color.

Value

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

See also

view.pdb(), pdb2ngl(), NGLVieweR::NGLVieweR(), bio3d::read.pdb()

Author

Barry Grant, bjgrant@ucsd.edu

Examples

  #pth <- "~/Desktop/courses/BIMM143/class10/pdbs/split_chain/"
  #files <- list.files(path=pth, full.names = TRUE)
  #pdbs <- bio3d::pdbaln(files, fit=TRUE, exefile="msa")

 data(transducin, package="bio3d")
 attach(transducin)
#> The following objects are masked from transducin (pos = 3):
#> 
#>     annotation, core, pdbs
#> The following objects are masked from transducin (pos = 4):
#> 
#>     annotation, core, pdbs
#> The following objects are masked from transducin (pos = 9):
#> 
#>     annotation, core, pdbs
#> The following objects are masked from transducin (pos = 10):
#> 
#>     annotation, core, pdbs

 view.pdbs2(pdbs)
#> Warning: Not ennough distinct colors for each structure, recycling

 view.pdbs2(pdbs, representation = "cartoon")
#> Warning: Not ennough distinct colors for each structure, recycling

 view.pdbs2(pdbs, colors = c("red","blue") )
#> Warning: Not ennough distinct colors for each structure, recycling