make.3D.Sphere {SpacePAC} | R Documentation |
Plots a sphere of radius r centered at a specific residue. Currently only 1 sphere can be plotted. The rgl pckage is required.
make.3D.Sphere(position.matrix, center, radius, alpha = 0.5)
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 |
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. |
The rgl package is called and a graph is shown.
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
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
## 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)