How to set the amino acid with special color?

[virologist]

Hi, Su

How to set certain amino acids with a special color?
See this demo trimer protein with 6 chains, including HA1: A, C, and E; HA2: B, D, and F.
My purpose is set the 206:220 on HA1 with red color (#e41a1c).
So, I try to use m_add_style and m_add_surface. But they look like do not as work as my desire.
Is there something wrong with my code?

rm(list=ls()); gc()
library(bio3d)
library(r3dmol)

p <- r3dmol() %>%
  m_add_model(data = m_fetch_pdb("6D7U", save.pdb = TRUE)) %>%
  m_add_model(data = m_bio3d(pdb)) %>%
#   m_set_style(style = m_style_cartoon(color = 'spectrum', ribbon = TRUE)) %>%
  m_set_style(style = m_style_cartoon()) %>% 
  m_add_outline() %>% 
#   m_set_style(style = c(m_style_cartoon(color = "spectrum", ribbon = TRUE), m_style_line())) %>% 
  m_add_surface(atomsel = m_sel(chain =c('A', 'B')), style = m_style_surface(opacity = 0.9, colorScheme="chain")) %>% 
  m_add_style(sel = m_sel(resi = c(206:220), chain="E"), style = m_style_sphere(scale = 0.5, color = "#e41a1c")) %>%
#   m_set_style(sel = m_sel(resi = c(206:220), chain = "A", byres = TRUE), style = m_style_cartoon(color = "red")) %>%
  m_add_surface(atomsel = m_sel(resi = c(206:220), chain = "C"), style = m_style_surface(opacity = 0.9, color = "#e41a1c")) %>%
#   m_add_line(start = m_sel(resi = 1:10, chain = "A"), end = m_sel(resi = 1:10, chain = "B"), spec = list(dashed = TRUE)) %>%
  m_add_label(text = "Site A", sel = m_sel( resi = 206:220, chain = "C"), style = m_style_label(borderColor = "green", borderThickness = 1, inFront = FALSE)) %>%
#   m_zoom_to(sel = m_sel(resi = c(206:220), chain = "A"))
#   m_set_zoom_limits(upper = 200, lower = 30)
    m_zoom_to()
p

Thanks,
Yang

[BradyAJohnston]

Hi Yang!

Thanks for the bug report. I've poked around and found that the problem is not your code, but a bug. It seems to be coming a result of the default that we have set for the colorscheme.

At the moment for all of the m_style_*() functions it is:

colorScheme="default"

So when you are setting the style with:

m_style_sphere(scale = 0.5, color = "#e41a1c")

Even though you have set a specific colour it is being overriden by the default colorScheme = "default".

I will fix this, but as a workaround for you code at the moment to get it working, you can override the colorScheme
default by:

m_style_sphere(scale = 0.5, color = "#e41a1c", colorScheme = NULL)

Adjusting your code with the workaround:

rm(list = ls())
gc()
library(bio3d)
library(r3dmol)

p <- r3dmol() %>%
  m_add_model(data = m_fetch_pdb("6D7U", save.pdb = TRUE)) %>%
  m_add_model(data = m_bio3d(pdb)) %>%
  #   m_set_style(style = m_style_cartoon(color = 'spectrum', ribbon = TRUE)) %>%
  m_set_style(style = m_style_cartoon()) %>% 
  m_add_outline() %>% 
  #   m_set_style(style = c(m_style_cartoon(color = "spectrum", ribbon = TRUE), m_style_line())) %>% 
  m_add_surface(atomsel = m_sel(chain =c('A', 'B')), style = m_style_surface(opacity = 0.9, colorScheme="chain")) %>% 
  m_add_style(sel = m_sel(resi = c(206:220), chain="E"), style = m_style_sphere(scale = 0.5, color = "#e41a1c", colorScheme = NULL)) %>%
  #   m_set_style(sel = m_sel(resi = c(206:220), chain = "A", byres = TRUE), style = m_style_cartoon(color = "red")) %>%
  m_add_surface(atomsel = m_sel(resi = c(206:220), chain = "C"), style = m_style_surface(opacity = 0.9, color = "#e41a1c", colorScheme = NULL)) %>%
  #   m_add_line(start = m_sel(resi = 1:10, chain = "A"), end = m_sel(resi = 1:10, chain = "B"), spec = list(dashed = TRUE)) %>%
  m_add_label(text = "Site A", sel = m_sel( resi = 206:220, chain = "C"), style = m_style_label(borderColor = "green", borderThickness = 1, inFront = FALSE)) %>%
  #   m_zoom_to(sel = m_sel(resi = c(206:220), chain = "A"))
  #   m_set_zoom_limits(upper = 200, lower = 30)
  m_zoom_to()
p

I hope this is what you are after at the moment, and thanks so much for the bug report! We really appreciate it :)

[virologist]

works for me, thank you very much.