make.3D.Sphere: Plots a sphere centered at the specified amino acid with a specified radius.

Description

Plots a sphere of radius r centered at a specific residue. Currently only 1 sphere can be plotted. The rgl pckage is required.

Usage

make.3D.Sphere(position.matrix, center, radius, alpha = 0.5)

Arguments

position.matrix

A dataframe consisting of six columns: 1) Residue Name, 2) Amino Acid number in the protein, 3) Side Chain, 4) X-coordinate, 5) Y-coordinate and 6) Z-coordinate. Please see get.Positions and get.AlignedPositions in the iPAC package.

center

The residue number you want the sphere centered at. Use the number from the "Can.Count" column in the position matrix.

radius

The radius of the sphere you would like to draw.

alpha

The "darkness" of the sphere.

Value

The rgl package is called and a graph is shown.

References

Daniel Adler and Duncan Murdoch (2013). rgl: 3D visualization device system (OpenGL). R package version 0.93.935. http://CRAN.R-project.org/package=rgl

Examples

Run this code

## Not run: 
# #Plots a sphere centered around amino acid 12 with radius 3.
# library(rgl)
# 
# #loads the data
# CIF <- "http://www.pdb.org/pdb/files/3GFT.cif"
# Fasta <- "http://www.uniprot.org/uniprot/P01116-2.fasta"
# KRAS.Positions <- get.Positions(CIF, Fasta, "A")
# 
# #generates the plot
# make.3D.Sphere(KRAS.Positions$Positions, 12, 3)
# ## End(Not run)