Insufficient Statistics - 3D Structural Biology

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

It’s that easy! Now if you want to represent the structure with the ball and stick representation, you can do so:

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

Reuse

https://creativecommons.org/licenses/by/4.0/

Citation

BibTeX citation:

@online{dewitt2022,
  author = {Michael DeWitt},
  title = {3D {Structural} {Biology}},
  date = {2022-07-04},
  url = {https://michaeldewittjr.com/programming/2022-07-04-3d-structural-biology},
  langid = {en}
}

For attribution, please cite this work as:

Michael DeWitt. 2022. “3D Structural Biology.” July 4, 2022. https://michaeldewittjr.com/programming/2022-07-04-3d-structural-biology.