How to control colour map of proteins visualized in a Jupyter notebook cell?

[SinaSarparast]

Hello,

I'm trying to visualize proteins in a jupyter notebook cell using nglview. By default the colouring theme used is based on the structures. I want to use bfactor as a coloring scheme. I can do that in the nglviewer app from the panel, but in a notebook environment I don't know how to set the right attributes to get the same results as I get when I use the app.
It's very helpful if someone can direct me to the relevant documentation or examples that can help me do so?

Thanks,

[hainm]

hi @SinaSarparast

Can you do something like view.add_cartoon(color='bfactor')?

[SinaSarparast]

Hi @hainm ,

Thanks for the answer. I've managed to fix the issue with the following

view = nv.show_biopython(structure)
view.remove_cartoon() # to remove previous visualization
view.add_representation(
repr_type="ribbon",
colorScheme= "bfactor", colorScale= "spectral", colorReverse= 1
)
view

where can I find more information on the colorScale? We are replacing prediction errors with the bfactor, so some values can be negative, and we scale it to [-1,1]. Is there a good colorScale that covers negative values as well?

[hainm]

where can I find more information on the colorScale? We are replacing prediction errors with the bfactor, so some values can be negative, and we scale it to [-1,1]. Is there a good colorScale that covers negative values as well?

I am not sure below will answer your question, but you can see different value for colorScale from the app.

[meneshail]

Hi @hainm ,

Thanks for the answer. I've managed to fix the issue with the following

view = nv.show_biopython(structure)
view.remove_cartoon() # to remove previous visualization
view.add_representation(
repr_type="ribbon",
colorScheme= "bfactor", colorScale= "spectral", colorReverse= 1
)
view

where can I find more information on the colorScale? We are replacing prediction errors with the bfactor, so some values can be negative, and we scale it to [-1,1]. Is there a good colorScale that covers negative values as well?

Hi,

I had the same question this week and checked the source codes of ngl. It turns out when the Colormaker is constructed it will first iterate over each atom to decide the min and max. This will be used as the domain parameter later on. So basically your bfactors will be normalized with a min-max scaler to fit in the [0, 1] range that the colormap uses.

https://github.com/nglviewer/ngl/blob/beb8bf93c001fd36a60a2bf6185f1aa5d503f4d3/src/color/bfactor-colormaker.ts#L34-L50

if (!params.domain) {
  let selection
  let min = Infinity
  let max = -Infinity


  if (params.sele) {
    selection = new Selection(params.sele)
  }


  params.structure.eachAtom(function (a) {
    const bfactor = a.bfactor
    min = Math.min(min, bfactor)
    max = Math.max(max, bfactor)
  }, selection)


  this.parameters.domain = [ min, max ]
}