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

In gryslik/SpacePAC: Identification of Mutational Clusters in 3D Protein Space via Simulation.

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.

Note

This function is made for ease of use in preliminary analysis only. For more sophisticated graphing packages, consider using PyMol at: http://www.pymol.org

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

See Also

get.Positions

Examples

## Not run: 
#Plots a sphere centered around amino acid 12 with radius 3.
library(rgl)

#loads the data
CIF <- "https://files.rcsb.org/view/3GFT.cif"
Fasta <- "https://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)

gryslik/SpacePAC documentation built on May 4, 2019, 3:13 a.m.