Bios2cor (version 1.2)

write_pdb: PDB and PML file creation for 3D representation of PCA analysis

Description

Given a PCA structure, creates .pdb and .pml files for 3D visualization with Pymol

Usage

write_pdb(pca, trio_comp= c(1:3), pdb_filepath, pml_filepath)

Arguments

pca

An object created by the centered_pca function

trio_comp

A numeric vector of length 3 indicating the principal components to be displayed. Default is c(1, 2, 3).

pdb_filepath

A string of characters indicating the full path name of the output PDB file.

pml_filepath

a string of characters indicating the full path name of the output PML file for visualization with Pymol.

Value

Returns two files: a PDB file which contains three PCA coordinates for each element in PDB format and a PML file for nice visualization with Pymol.

Details

This function creates PDB and PML files to visualize the positions of the elements (sequence positions or dihedral angles) in a 3D space corresponding to three selected components of the PCA space. The PDB file can be viewed in any molecular graphics softaware. The PML file allows a nice representation with Pymol (axis, background color, size of points and for GPCRs, color code for helices).

Examples

# NOT RUN {
  align <- import.msf(system.file("msa/toy_align.msf", package = "Bios2cor"))

  #Creating OMES object
  omes <- omes(align)
  omes <- omes$normalized
  
  # Creating PCA structures for OMES method 
  pca <- centered_pca(omes, m=NULL, pc= NULL, dec_val= 5,eigenvalues_csv= NULL)

  #Creating PDB and PML files (open PDB file with Pymol then "File > Run" PML file)
  indices <- c(1,2,3)
  write_pdb(pca, indices, "pdb_file.pdb", "pml_file.pml")
# }