ppi.pymol: Write PyMOL file for protein-protein interaction data

In egmg726/crisscrosslinker: An R package for protein interaction analysis

Description

Generates a file for PyMOL based on the XL sites aligned to PDB structures.

Usage

ppi.pymol(
  xlink.df.pdb,
  list_of_start_and_end_pdbs = NULL,
  show_only_real_structures = NULL,
  write_file = TRUE,
  colors = NULL,
  color_by = "freq",
  experiment_directory = NULL,
  pdb_numbering = FALSE,
  file.name = "xlink.pml",
  start.num = 1
)

Arguments

xlink.df.pdb	data.frame output from ppi.matchPDB() or ppi.matchPDB2()
show_only_real_structures	A list of proteins to only show "real" structrures as opposed to 2D generated structures. Not relevant unless using generated structures.
write_file	If TRUE, will write the produced .pml file.
colors	A list of colors as R names or hexcodes or a palette defined by RColorBrewer/viridis. If left blank, will use the colors that are in the column freq_color.
color_by	If colors is not NULL, choose either 'freq' or 'dist' for which variable should be colored.
file.name	File name for the exported PyMOL file. Should end in '.pml'
start.num	Starting number for custom color, change if additional custom colors are being used

egmg726/crisscrosslinker documentation built on Jan. 23, 2021, 1:50 a.m.