Representations
Surfaces, nucleic acids, and glycans
Use specialized representations where molecular context needs a different shape language.
Surface
surface has a molecular surface kind and a presentation style. The current public values are van_der_waals, solvent_accessible, solvent_excluded, and gaussian; styles are solid, contour, dots, filled_contour, and mesh.
import molframe
import molgfx
structure = molframe.read("4hhb.cif").infer_bonds()
scene = molgfx.Scene(structure)
scene.add(molgfx.rep.surface(
target="chain A",
kind="solvent_accessible",
style="mesh",
probe_radius=1.6,
opacity=0.55,
color=(49, 104, 142),
))Use a focused selection rather than an entire large assembly when the overlay question is local.
Nucleic acids and glycans
# Each target selects nothing on a protein-only entry such as 4HHB and raises
# SpecError; use an entry with nucleic acid and glycans. `nucleicbase` also needs
# the chemical-component annotations that the deposited file carries.
scene.add(molgfx.rep.nucleic_acid(target="nucleic", width=1.4))
scene.add(molgfx.rep.bases(target="nucleicbase", radius=0.3))
scene.add(molgfx.rep.glycan(target="saccharide", width=1.5))base_pairs adds paired base context; glycan uses the glycosidic-tree representation. These targets are MolFrame queries; see Writing queries and commands.