Style

Presets

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. required
Selection Bool True
Preset Int Switch between preset styles 1
Quality Int QUality of the style, hgher is better quality 3
Shade Smooth Bool Whether to shade the resulting geometry smoothe True
Material Material Material to use on the resulting geoemtry MN Default

Outputs

Name Type Description Default
Geometry Geometry required

Spheres

Style to apply the traditional space-filling atomic representation of atoms. Spheres are scaled based on the vdw_radii attribute. By default the Point Cloud rendering system is used, which is only visible inside of Cycles.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges. required
Selection Bool Selection for applying the style. Unselected is discarded. True
EEVEE Bool Use Eevee or Cycles compatible atoms. False
Radii Float Scale the vdw_radii of the atoms. 0.8
Subdivisions Int Subdivisions for Eevee compatible atoms. 2
Shade Smooth Bool Shade Eevee compatible atoms smooth. True
Material Material Material to apply to resulting style. MN Default

Outputs

Name Type Description Default
Geometry Geometry required

Cartoon

Style to apply the traditional cartoon representation of protein structures. This style highlights alpha-helices and beta-sheets with arrows and cylinders.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges. required
Selection Bool Selection for applying the style. Unselected is discarded. True
Quality Int Number of subdivisions, ‘quality’ of the cartoon. 2
Smooth / Sharp Bool Create smooth or sharp style cartoon geometry. False
Arrows Bool Create arrows for beta-sheet cartoons. True
Cylinders Bool Create cylinders for alpha-helix geometry. False
Thickness Float Thickness of the secondary structure geometry. 0.4
Width Float Width of the secondary structure geometry. 1.8
Loop Radius Float Radius of the loop geometry. 0.18
BS Smooth Float Factor 0 -> 1, amount to flatten the beta-sheets. 0.5
Interpolate Color Bool Interpolate between the different color values True
Shade Smooth Bool Shade the resulting geometry smooth. True
Material Material Material to apply to resulting style. MN Default

Outputs

Name Type Description Default
Geometry Geometry required

Ribbon

Style that creates a continuous solid ribbon or licorice tube through the backbones of peptides and nucleic acids.

Inputs

Name Type Description Default
Atoms Geometry required
Selection Bool True
Quality Int 3
Radius Float 1.6
BS Smoothing Float 0.5
Interpolate Color Bool True
Shade Smooth Bool True
Material Material MN Default

Outputs

Name Type Description Default
Geometry Geometry required

Surface

Style that creates a surface representation based on the proximity of atoms to a probe that is moved through the entire structure.

Inputs

Name Type Description Default
Atoms Geometry required
Selection Bool True
Quality Int Quailty of the surface to generate 3
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 10
Color by CA Bool Only take colors from CA atoms (or similar in nucleic acids) True
Color Blur Int When coloring the surface, blur colors from nearby atoms 2
Shade Smooth Bool True
Material Material MN Default

Outputs

Name Type Description Default
Geometry Geometry required
Instances Geometry required

Ball And Stick

Style that creates cylinders for bonds and spheres for atoms. The atoms can be either Eevee or Cycles compatible, with customisation to resolution and radius possible.

Inputs

Name Type Description Default
Atoms Geometry Atomic geometry that contains vertices and edges. required
Selection Bool True
Sphere EEVEE Bool True
Sphere Radii Float 0.3
Sphere Subdivisions Int 2
Bond Resolution Int 6
Bond Radius Float 0.3
Shade Smooth Bool True
Material Material MN Default

Outputs

Name Type Description Default
Geometry Geometry required

Stick

Style that creates a cylinder for each bond. Cylindrical caps to the cylinders are currently not supported. Best to use MN_style_ball_and_stick.

Inputs

Name Type Description Default
Atoms Geometry required
Selection Bool True
Radius Float 0.2
Quality Int 2
Mix Color Bool False
Shade Smooth Bool True
Material Material MN Default

Outputs

Name Type Description Default
Geometry Geometry required