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
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Sphere Geometry |
Point | 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. |
Sphere Radii |
0.8 | Scale the vdw_radii of the atom when setting the radius of the spheres |
Sphere Subdivisions |
2 | Number of subdicisions when using Instances or Mesh to represent atoms |
Shade Smooth |
True | Apply smooth shading when using Instances or Mesh |
Material |
None | Material to apply to the resulting geometry |
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.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
2 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Peptide DSSP |
False | Use the DSSP algorithm to compute the sec_struct attribute |
Peptide Cylinders |
False | Use cylinders for helices instead of ribbons |
Peptide Arrows |
True | User arrows for sheets |
Peptide Rounded |
False | Create rounded sheets and helices |
Peptide Thickness |
0.6 | Thickness for the sheets and helices |
Peptide Width |
2.2 | Width for the sheets and helices |
Peptide Loop Radius |
0.3 | Radius of the loops for unstructure regions |
Peptide Smoothing |
0.5 | Smoothing to apply to sheets |
Backbone Shape |
Cylinder | |
Backbone Radius |
2.0 | |
Base Shape |
Rectangle | |
Base Realize |
False | |
Color Blur |
True | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
Style Ribbon
A simplified tube that through the alpha carbons of the protein. Controls for the raadius and smoothing of sheets are available.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Curves |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Backbone Smoothing |
0.5 | Smoothen the sheet ribbons such as beta-sheets |
Backbone Threshold |
4.5 | Distance (Angstroms) over which subsequent CA points are treated as a new chain |
Backbone Radius |
1.6 | |
Backbone Shape |
Cylinder | |
Backbone Radius |
2.0 | |
Base Geometry |
None | |
Base Scale |
[2.5, 0.5, 7.0] | |
Base Resolution |
4 | |
Base Realize |
False | |
UV Map |
False | Compute and store the uv_map for the final protein ribbon geometry |
U Component |
Factor | |
Color Blur |
True | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Scale Radii |
1.5 | Scale the VDW radii of the atoms when creating the surface |
Probe Size |
1.0 | Size of the probe that is used to check for solvent accessibility (Angstroms) |
Relaxation Steps |
10 | Number of times smoothening is applied to the generate surface stretched between the atoms |
Separate By |
chain_id | |
Group ID |
0 | |
Color Source |
Alpha Carbon | |
Color Blur |
2 | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Quality |
2 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Sphere Geometry |
Instance | 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. |
Sphere Radii |
0.3 | Scale the vdw_radii attribute before setting the radius for the spheres |
Bond Split |
False | Split apart double and triple bonds visually |
Bond Find |
False | 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 Radius |
0.3 | Set the radius for the generated bonds in Angstroms |
Color Blur |
False | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
Style Sticks
Each bond terminates cleanly in a half sphere for a typical stick representation of the atoms and bonds
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Radius |
0.2 | Radius of the sticks in Angstroms |
Color Blur |
False | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Color Blur |
False | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Color Blur |
False | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |
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.
Outputs
| Description | Socket |
|---|---|
| The generated geometry for the style node group | Geometry |
Inputs
| Socket | Default | Description |
|---|---|---|
Atoms |
None | Atomic geometry that contains vertices and edges |
Selection |
True | Selection of atoms to apply this style to, discarding unselected points |
Quality |
3 | A lower value results in less geometry, with a higher value meaning better looking but more dense geometry |
Color Blur |
True | Interpolate between colors when enabled. When disabled the faces will take their color from their corresponding atom without interpolating |
Shade Smooth |
True | Apply smooth shading to the created geometry |
Material |
None | Material to apply to the resulting geometry |