Style

Style Spheres

Space filling atomic spheres scaled based on their vdw_radii attribute. By default they are Point Clouds which don’t render well inside of EEVEE, but are extremely fast to render and manipulate inside of Cycles. To show the atoms inside of EEVEE you can enable the As Mesh input which realises them into real geometry

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Sphere As Mesh Bool Create real geometry by instancing and realising icospheres. By default this is disabled and the points are a Point Cloud False
Sphere Radii Float Scale the vdw_radii of the atom when setting the radius of the spheres 0.8
Sphere Subdivisions Int Subdivisions for Eevee compatible atoms. None
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Cartoon

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 DSSP input, but this will differ to secondary structure imported from structures from the PDB.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
DSSP Bool Use the DSSP algorithm to compute the sec_struct attribute False
Cylinders Bool Use cylinders for helices instead of ribbons False
Arrows Bool User arrows for sheets True
Rounded Bool Create rounded sheets and helices False
Thickness Float Thickness for the sheets and helices 0.6
Width Float Width for the sheets and helices 2.2
Loop Radius Float Radius of the loops for unstructure regions 0.3
Smoothing Float Smoothing to apply to sheets 0.5
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating True
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Ribbon

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 Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Radius Float 1.6
Smoothing Float Smoothen the sheet ribbons such as beta-sheets 0.5
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating True
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Surface

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 Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Separate Bool Whether to create separate surfaces, based on the ‘Attribute’ name True
Attribute String Attribute to separate the surface by chain_id
Scale Radii Float Scale the VDW radii of the atoms when creating the surface 1.5
Probe Size Float Size of the probe that is used to check for solvent accessibility (Angstroms) 1.0
Triangulate Bool Whether to triangulate the resulting mesh. Can help reduce shading problems False
Relaxation Steps Int Number of times smoothening is applied to the generate surface stretched between the atoms None
Color by CA Bool Only take colors from CA atoms (or similar in nucleic acids) True
Color Blur Int Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating None
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None
Instances Geometry The resulting geometry of the style. Each chain is a separate instance. None

Style Ball and Stick

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 Sheres 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 Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Sphere As Mesh Bool Render spheres as real mesh geometry instead of point clouds True
Sphere Radii Float Scale the vdw_radii attribute before setting the radius for the spheres 0.3
Bond Split Bool Split apart double and triple bonds visually False
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 False
Bond Radius Float Set the radius for the generated bonds in Angstroms 0.3
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating False
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Sticks

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

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Radius Float Radius of the sticks in Angstroms 0.2
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating False
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Preset 1

Quickly switch between several different pre-made preset styles. Best used when using MolecularNodes via scripts, ensuring all atoms are displayed using a combination of cartoons and atoms.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating False
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Preset 2

Quickly switch between several different pre-made preset styles. Best used when using MolecularNodes via scripts, ensuring all atoms are displayed using a combination of cartoons and atoms.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating False
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Preset 3

Quickly switch between several different pre-made preset styles. Best used when using MolecularNodes via scripts, ensuring all atoms are displayed using a combination of cartoons and atoms.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None

Style Preset 4

Quickly switch between several different pre-made preset styles. Best used when using MolecularNodes via scripts, ensuring all atoms are displayed using a combination of cartoons and atoms.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges None
Selection Bool Selection of atoms to apply this style to, discarding unselected points True
Quality Int A lower value results in less geometry, with a higher value meaning better looking but more dense geometry None
Color Blur Bool Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating True
Shade Smooth Bool Apply smooth shading to the created geometry True
Material Material Material to apply to the resulting geometry None

Outputs

Name Type Description Default
Geometry Geometry The generated geometry for the style node group None