README.md

Status:

Documentation:

Installation

To install BioMakie, access the Julia package manager by pressing ] from the Julia REPL, then run add BioMakie.

Contributing and questions

Anyone can contribute to this package, by doing things like reporting bugs, fixing issues, improving performance, adding new features, and adding examples. Feel free to open an Issue or Pull Request, or communicate on the #biology or #makie channels of the Julia Slack.

About

This package provides plotting functions for protein structures, multiple sequence alignments, and some other related plots like protein structure contact maps. It also provides more complicated examples that show off additional functionality and interfaces. The main plotting functions are plotstruc and plotmsa, along with their mutating versions, plotstruc! and plotmsa!.

using BioMakie
using GLMakie
using BioStructures
struc = retrievepdb("2vb1") |> Observable
## or
struc = read("2vb1.pdb", BioStructures.PDBFormat) |> Observable

fig = Figure()
plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors)
plotstruc!(fig, struc; plottype = :covalent, gridposition = (1,2))

To view a multiple sequence alignment, use the plotmsa function with a Pfam MSA or fasta file.

using FASTX
reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")
msa = [reader...] |> Observable
close(reader)
## or 
using MIToS.MSA
msa = read_file("pf00062.stockholm.gz", Stockholm)

fig = plotmsa(msa; colorscheme = :tableau_blue_green)

Other examples

Viewing the frequencies of amino acids in a multiple sequence alignment

Alpha shapes can be used to visualize the surface of a protein structure

Database information can be displayed for a protein (including a GPT response, OpenAI.jl)

Protein residue mutation and changing rotamers (with ProtoSyn.jl)