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This is just a short blurb to mention the r3dmol package which allows users to render the 3D representation of pdb files of different biological structures.

Example with Neisseria gonorrhoeae

I am interested in generating some of the structures of Neisseria gonorrhoeae, the pathogen responsible for the sexually transmitted infection, gonorrhea. I can go over to the protein data bank and do a search and find some of the available structures.

ng_pdb <- "https://files.rcsb.org/download/4R1I.pdb"

download.file(ng_pdb, destfile = "4R1I.pdb")

ng_pdb <- readLines("4R1I.pdb")

Now for the magical part:

library("r3dmol")
m1 <- r3dmol(                         # Set up the initial viewer
  viewer_spec = m_viewer_spec(
    cartoonQuality = 10,
    lowerZoomLimit = 50,
    upperZoomLimit = 350
  )
) %>%
  m_add_model(                  # Add model to scene
    data = ng_pdb,
    format = "pdb"
  ) %>%
  m_zoom_to() %>%               # Zoom to encompass the whole scene
  m_set_style(                  # Set style of structures
    style = m_style_cartoon(
      color = "#00cc96"
    )
  )%>%
  m_set_style(                  # Set style of specific selection
    sel = m_sel(ss = "s"),      # (selecting by secondary)
    style = m_style_cartoon(
      color = "#636efa",
      arrows = TRUE
    )
  ) %>%
  m_set_style(                  # Style the alpha helix
    sel = m_sel(ss = "h"),      # (selecting by alpha helix)
    style = m_style_cartoon(
      color = "#ff7f0e"
    )
  ) %>%
  m_rotate(                     # Rotate the scene by given angle on given axis
    angle = 90,
    axis = "y"
  ) %>%
  m_spin()

m1

m1 %>%
 m_set_style(style = m_style_stick())