How to visualize electron density of a specific part of the protein residue?

Question

Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I can't do that, because for nglview I need to have a special Object. As I'm a newbie, I'd like to address this question to specialists.

At the moment I'm trying to visualise model (structure), not electron density. But the next step is trying to find a package to visualize electron density also. I've just started becoming familiar with some open packages.

Thank You in Advance!

Answer 1

NGLview runs off the JavaScript libray NGL, which is documented as a series of very helpful examples: in the gallery. The commands are not one-to-one (slightly frustratingly), but it is helpful as you can figure it out easily with a few dir and help commands. In this case whatever example of density being loaded it will reveals that it's a different component —this is the same everywhere as density files do not contain atomic coordinates. Unfortunately, there's not a direct way to generate a new ComponentViewer from different sources to an NGLWidget and you cannot merge two of them: the various .show_* functions return an NGLWidget but aren't part of it.

First, I am not sure why you are going through a convoluted route for loading a PDB code:

pdb_code = '1fat'

import nglview as nv

view: nv.NGLWidget = nv.show_pdbid(pdb_code) 

Now, on loading the component a representation is added to it. These can hide the representation you then add and things will not make sense, until this detail is recalled! I fall in that pit nearly every time. But we can change it with update command:

# I don't like wonky sheets
view.update_cartoon(smoothSheets=True, color='salmon', component=0)

Now let's add the density map the circuitous way (no .show_url).

import requests, io
response: requests.Response = requests.get('https://www.ebi.ac.uk/pdbe/coordinates/files/1fat.ccp4')
response.raise_for_status()
fh = io.BytesIO(response.content)
comp: nv.component.ComponentViewer = view.add_component(fh, ext='ccp4') 

Now we can add a surface representation, but first let's clear the default. For the arguments I had a gander at the example:

view.clear_representations(component=1)
view.add_representation('surface', 
                        color='grey', 
                        wireframe=True, 
                        isolevel=1.5,
                        component=1)
view.center('100-110:A')
view