Proteins and Surfaces¶

Protein Input¶

Create a COSMolKit protein from PDB or mmCIF text:

from cosmolkit import Protein
from cosmol_viewer import Scene, Cartoon, Surface

cif = open("protein.cif", encoding="utf-8").read()
protein = Protein.from_mmcif(cif)

pdb = open("protein.pdb", encoding="utf-8").read()
protein_from_pdb = Protein.from_pdb(pdb)

COSMolKit parses the structure and the viewer assigns secondary structure from backbone geometry before generating a ChimeraX-style cartoon ribbon.

Cartoon Ribbons¶

scene = Scene()
scene.add(protein)  # default Cartoon
scene.set("rainbow", protein, Cartoon().rainbow_residues())

rainbow_residues() colors every biopolymer chain independently from its first to last rendered residue. Use color() for a uniform ribbon color.

Molecular Surfaces¶

Surface() configures a molecular surface. Set solvent_accessible=True for a solvent-accessible representation.

surface = Surface().configure(
    probe_radius=1.4,
    grid_spacing=0.5,
    solvent_accessible=False,
    sharp_boundaries=True,
).color("#dce8f2").opacity(0.9)

Smaller grid spacing produces a denser mesh and increases surface generation cost. sharp_boundaries=True subdivides atom patches so shared boundaries are exact.

Combining Representations¶

Reuse the same Protein for a ribbon and surface. The binding imports it only once while the scene or a selection retains it:

from cosmol_viewer import Scene

scene = Scene()
scene.add(protein)
scene.add(protein, surface)
scene.set_depth_cue(True)