Proteins and Surfaces¶

Protein Input¶

Create a protein shape from PDB or mmCIF text:

from cosmol_viewer import Protein

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

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

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

Cartoon Ribbons¶

ribbon = protein.ribbon().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() creates a solvent-excluded surface with a 1.4 angstrom probe and 0.5 angstrom grid spacing. solvent_accessible_surface() creates the corresponding solvent-accessible representation.

surface = (
    Protein.from_mmcif(cif)
    .centered()
    .surface_with_options(
        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¶

Separate Protein values can show a ribbon and a translucent surface in the same scene:

from cosmol_viewer import Scene

scene = Scene()
scene.add_shape(ribbon)
scene.add_shape(surface)
scene.set_depth_cue(True)