Style

Generate geometry for the different molecular styles

Style Ball and Stick

Video

Shows the atoms and bonds. The bonds are cylinders between the atoms, which can be split apart for double and triple bonds if the information is within the structure on import. Spheres can be displayed as mesh of as Point Cloud as with the Style Spheres node. Bonds can also be calculated if none are present, but this is approximate and purely distance based so should not be relied upon

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry
Sphere Menu Show spheres as a Point Cloud, Instances of a mesh Icosphere, or realised Mesh instances of an Icosphere. Point cloud is best for performance and should definitely be used if rendering in Cycles.
Scale Float Scale the vdw_radii attribute before setting the radius for the spheres
Bond Split Menu
Bond Scale Float Set the radius for the generated bonds in Angstroms
Bond Find Bool Find possible bonds for the selected atoms based on a distance search. Unselected atoms maintain any bonds they already have. Bonds that are found are all treated as single bonds
Bond Find Scale Float Scale the VDW radii of the atoms when searching for bonds
Shade Smooth Bool Apply smooth shading to the created geometry
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleBallAndStick

Style Cartoon

Video

Peptide helices and sheets are emphasized with the ‘traditional’ cartoon style. Secondary structure becomes distinct and nucleic acids become a simplified representation. The node also includes an option to calculate secondary structure by enabling the Topology DSSP input, but this will differ to secondary structure imported from structures from the PDB.

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry
Peptide Shape Menu Create rounded sheets and helices
Helix Shape Menu Use cylinders for helices instead of ribbons
Helix Thickness Float Thickness for the sheets and helices
Helix Width Float Width for the sheets and helices
Sheet Arrows Menu User arrows for sheets
Sheet Thickness Float
Sheet Width Float
Sheet Smoothing Float Smoothing to apply to sheets
Loop Radius Float Radius of the loops for unstructure regions
Backbone Shape Menu
Nucleic Width Float
Nucleic Thickness Float
Nucleic Radius Float
Base Shape Menu
Base Scale Cylinder Vector
Base Scale Rectangle Vector
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating
Shade Smooth Bool Apply smooth shading to the created geometry
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleCartoon

Style Ribbon

Video

A simplified tube that through the alpha carbons of the protein. Controls for the raadius and smoothing of sheets are available.

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry
Peptide Radius Float
Backbone Smoothing Float Smoothen the sheet ribbons such as beta-sheets
Backbone Threshold Float Distance (Angstroms) over which subsequent CA points are treated as a new chain
UV Map Bool Compute and store the uv_map for the final protein ribbon geometry
U Component Menu Store either the ‘Length’ or the ‘Factor’ of the curve as the U component.
Nucleic Backbone Shape Menu
Nucleic Backbone Radius Float
Nucleic Backbone Width Float
Nucleic Backbone Thickness Float
Base Geometry Geometry
Base Scale Vector
Base Resolution Int
Base Realize Bool
Shade Smooth Bool Apply smooth shading to the created geometry
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleRibbon

Style Spheres

Video

Space filling atomic spheres scaled based on their vdw_radii attribute. By default they are Point Clouds which render as simple primitives inside of EEVEE but perfect spheres inside of Cycles. To show the atoms inside of EEVEE you can choose the Instance or Mesh as the sphere type, which will generate traditional polygonal geometry for rendering in EEVEE.

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Sphere Menu Show spheres as a Point Cloud, Instances of a mesh Icosphere, or realised Mesh instances of an Icosphere. Point cloud is best for performance and should definitely be used if rendering in Cycles.
Quality Int Number of subdicisions when using Instances or Mesh to represent atoms
Scale Float Scale the vdw_radii of the atom when setting the radius of the spheres
Shade Smooth Bool Apply smooth shading when using Instances or Mesh
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleSpheres

Style Sticks

Video

Each bond terminates cleanly in a half sphere for a typical stick representation of the atoms and bonds

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Sphere Menu Show spheres as a Point Cloud, Instances of a mesh Icosphere, or realised Mesh instances of an Icosphere. Point cloud is best for performance and should definitely be used if rendering in Cycles.
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry
Scale Float Radius of the sticks in Angstroms
Shade Smooth Bool Apply smooth shading to the created geometry
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleSticks

Style Surface

Video

The vdw_radii and a probe are used to calculate the surface of the molecule. This is still a close approximation of other surface generation algorithms and won’t match those made by PyMol and ChimeraX exactly. Coloring of the surface is by default done by sampling the closest alpha carbon, but this can be disabled to use the closest atom for coloring the mesh

Inputs

Name Type Description
Atoms Geometry Atomic geometry that contains vertices and edges
Selection Bool Selection of atoms to apply this style to, discarding unselected points
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry
Scale Float Scale the VDW radii of the atoms when creating the surface
Relax Int
Offset Float Object-space distance to offset the SDF surface
Fillet Int Number of iterations to apply the filter
Mean Width Int Filter kernel radius in voxels
Mean Iterations Int Number of iterations to apply the filter
Separate By Menu
Group ID Int
Color Source Menu
Color Blur Int Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating
Shade Smooth Bool Apply smooth shading to the created geometry
Material Material Material to apply to the resulting geometry

Outputs

Name Type Description
Geometry Geometry The generated geometry for the style node group

API Reference: nodes.geometry.StyleSurface