rbd.pymol: Write PyMol file for RBDmap Data

Description Usage Arguments

View source: R/pdb_functions2.R

Description

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

Usage

1
2
3
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.


egmg726/crisscrosslinker documentation built on Sept. 8, 2018, 9:30 p.m.