Working with NGLView#

Creating multi-layered graphical representations, styling binding sites, and rendering surfaces in NGLView.

Effective scientific communication requires clear and expressive molecular figures. MolSysMT provides a direct bridge to NGLView, allowing you to combine diverse representations (cartoon backbones, licorice side-chains, transparent surfaces, contact cylinders, and vector arrows) with spatial precision.

In this recipe, we build an expressive multi-component visualization of T4 Lysozyme with its bound Benzene ligand, highlighting active pocket interactions and exporting the scene.

Added in version 1.0.0.

Loading Complex#

We load the high-resolution T4 Lysozyme L99A system from the MolSysMT bundled dataset:

import molsysmt as msm

# Load T4 Lysozyme with bound Benzene ligand
molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'], to_form='molsysmt.MolSys')
msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_ions	n_small_molecules	n_proteins	n_structures
molsysmt.MolSys	1441	302	141	6	141	5	136	2	2	1	1

Base Representation#

We convert the system to an interactive nglview.NGLWidget and standardize its camera viewport, background, and lighting:

# Convert to NGLWidget
view = msm.convert(molsys, to_form='nglview.NGLWidget')

# Apply standardized orientation and optimal lighting
msm.third_party.nglview.standardize_view(view)
msm.third_party.nglview.show_as_cartoon(view, selection='molecule_type=="protein"', color='silver')
view

Pocket Representation#

Next, we highlight the hydrophobic cavity residues surrounding the Benzene ligand using spatial selection syntax:

# Highlight binding pocket residues in licorice representation
pocket_sel = 'molecule_type=="protein" within 0.5 nm of group_name=="BNZ"'
msm.third_party.nglview.show_as_licorice(view, selection=pocket_sel)

# Highlight ligand in ball-and-stick representation
msm.third_party.nglview.show_as_balls_and_sticks(view, selection='group_name=="BNZ"')

# Add transparent solvent-accessible surface around the pocket
msm.third_party.nglview.show_as_surface(view, selection=pocket_sel, opacity=0.4)
view

Annotation Arrows#

We can overlay 3D vector arrows on the active view to denote principal axes, pocket orientation, or binding vectors:

# Draw a vector arrow indicating active pocket axis
msm.third_party.nglview.add_arrows(
    view,
    origin='atom_index==0',
    end='atom_index==20',
    color='#E74C3C',
    radius='0.4 angstroms'
)
view

Exporting HTML Scene#

Finally, we serialize the complete 3D scene into a standalone, interactive HTML file for web publishing or sharing with collaborators:

import os

# Export the interactive scene to HTML
html_file = 't4_lysozyme_scene.html'
msm.third_party.nglview.write_html(view, html_file)

print(f"HTML scene exported: {os.path.exists(html_file)} (size: {os.path.getsize(html_file)} bytes)")
if os.path.exists(html_file):
    os.remove(html_file)

HTML scene exported: True (size: 189326 bytes)