Function to take bio3d structure and use in the r3dmol app.
m_bio3d(pdb)bio3d object containing coordinates for desired structure
library(bio3d)
library(r3dmol)
# create bio3d object
pdb <- read.pdb("1bna")
#> Note: Accessing on-line PDB file
# inspect bio3d object
pdb
#>
#> Call: read.pdb(file = "1bna")
#>
#> Total Models#: 1
#> Total Atoms#: 566, XYZs#: 1698 Chains#: 2 (values: A B)
#>
#> Protein Atoms#: 0 (residues/Calpha atoms#: 0)
#> Nucleic acid Atoms#: 486 (residues/phosphate atoms#: 24)
#>
#> Non-protein/nucleic Atoms#: 80 (residues: 80)
#> Non-protein/nucleic resid values: [ HOH (80) ]
#>
#> Nucleic acid sequence:
#> CGCGAATTCGCGCGCGAATTCGCG
#>
#> + attr: atom, xyz, seqres, calpha, remark,
#> call
# load bio3d object into r3dmol
r3dmol() %>%
m_add_model(data = m_bio3d(pdb)) %>%
m_zoom_to()