October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How to do it...
3D structure protein alignment with bio3d can be done using the following steps:
- Load the library and the PDB structure files:
library(bio3d)a <- read.pdb(file.path(getwd(), "datasets", "ch3" ,"1xwc.pdb"))b <- read.pdb(file.path(getwd(), "datasets", "ch3", "3trx.pdb"))
- Then, carry out the alignment of the structures:
pdbs <- pdbaln(list("1xwc"=a,"3trx"=b), fit=TRUE, exefile="msa")
- Launch and render the alignment in PyMOL:
pymol_path = "/Users/macleand/miniconda2/bin/pymol"pymol(pdbs, exefile = pymol_path, type = "launch", as="cartoon")
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