make.3D.Sphere {SpacePAC} | R Documentation

## 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.

### 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)

[Package SpacePAC version 1.18.3 Index]