rbd.pymol: Write PyMol file for RBDmap Data

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

Description

This function makes a PyMOL file (.pml) that can be used to visualize data obtained from rdb.getBindingSeq()

Usage

rbd.pymol(
  bs_output,
  color_by = "binding_sequence",
  colors = NULL,
  file.name = "rbd_pymol.pml",
  write.file = TRUE,
  experiment.dir = NULL,
  gray0 = FALSE,
  heatmap = TRUE,
  assembly = 0,
  fetch = TRUE
)

Arguments

bs_output	Output from rbd.getBindingSeq()
color_by	The variable that will be used to determine color. Must a column in bs_output or use "freq" to color by frequency of amino acid position in binding sequences. Defaults to "binding_sequence".
colors	Colors to be used for color.pymol() function.
file.name	If write.file = T, name of the output file. Defaults to 'rbd_pymol.pml'
write.file	Boolean. If TRUE, will output file with name of file.name. If FALSE, will return file as list.
experiment.dir	Directory of experiment, where PDB files are. If left as NULL, will use current directory.
gray0	Boolean. If TRUE, will shift color scheme for frequency analysis and label 0s as "gray" in PyMOL.
assembly	Assembly number for PyMOL output that corresponds to RCSB database. Works for PyMOL 1.8 and above.

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