Color
Customise the colors of the structure using these nodes. The color for atoms are always set before using the Style nodes. The Style Cartoon, Style Surface and Style Ribbon nodes take their color information from the atoms that are used to generate them. There are nodes to generate colors for each chain, each residue. The setting of Color attribute is done using the Set Color attribute.
Set Color
Set the Color attribute on the point domain, based on the input Color field. The Selection field limits the setting of the color to the input Selection, with the unselected points keeping their current Color attribute
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Atoms | Geometry |
Atomic geometry that contains vertices and edges | None |
| Selection | Bool |
Selection of atoms to apply this node to | True |
| Color | Color |
Color to apply to the selected atoms | [0.162, 0.624, 0.196, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Atoms | Geometry |
Atomic geometry with an updated Color attribute |
None |
Color Chain
Pick colors that are used for each chain_id that is present in the structure. The inputs can also accept fields to generate colors for that chain based on upstream field evaluation. This node is generated on a per-structure basis, so will only be useful for the corresponding structure.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Chain A | Color |
Color to set for Chain A | [0.461, 0.6, 0.24, 1.0] |
| Chain B | Color |
Color to set for Chain B | [0.24, 0.6, 0.574, 1.0] |
| … | Color |
Color to set for Chain … | [0.6, 0.24, 0.467, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The colors based on chain_id |
[0.0, 0.0, 0.0, 0.0] |
Color Segment
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Segment A | Color |
Color to set for Ligand B | [0.461, 0.6, 0.24, 1.0] |
| Segment B | Color |
Color to set for Ligand B | [0.24, 0.6, 0.574, 1.0] |
| … | Color |
Color to set for Ligand … | [0.6, 0.24, 0.467, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The colors based on entity_id |
[0.0, 0.0, 0.0, 0.0] |
Color Entity
Choose the colors for the individual entities in the structure. If there are multiple copies of the same protein or molecule in the structure but in different conformations, it can helpt to color them based on their entity_id rather than individual chain_id values
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Entity A | Color |
Color to set for Entity A | [0.461, 0.6, 0.24, 1.0] |
| Entity B | Color |
Color to set for Entity B | [0.24, 0.6, 0.574, 1.0] |
| … | Color |
Color to set for Entity … | [0.6, 0.24, 0.467, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The colors based on entity_id |
[0.0, 0.0, 0.0, 0.0] |
Color Ligand
Choose the colors for individual ligands in the structure.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Ligand A | Color |
Color to set for Ligand B | [0.461, 0.6, 0.24, 1.0] |
| Ligand B | Color |
Color to set for Ligand B | [0.24, 0.6, 0.574, 1.0] |
| … | Color |
Color to set for Ligand … | [0.6, 0.24, 0.467, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The colors based on entity_id |
[0.0, 0.0, 0.0, 0.0] |
Color Element
Choose colors for the individual elements of the periodic table. The first 80 elements are listed, grouped into panels in chunks of 20 elements per panel for better organisation.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| H | Color |
Set the color for the element H | [1.0, 1.0, 1.0, 1.0] |
| He | Color |
Set the color for the element He | [0.851, 1.0, 1.0, 1.0] |
| Li | Color |
Set the color for the element Li | [0.8, 0.502, 1.0, 1.0] |
| Be | Color |
Set the color for the element Be | [0.761, 1.0, 0.0, 1.0] |
| B | Color |
Set the color for the element B | [1.0, 0.71, 0.71, 1.0] |
| C | Color |
Set the color for the element C | [0.565, 0.565, 0.565, 1.0] |
| N | Color |
Set the color for the element N | [0.188, 0.314, 0.973, 1.0] |
| O | Color |
Set the color for the element O | [1.0, 0.051, 0.051, 1.0] |
| F | Color |
Set the color for the element F | [0.565, 0.878, 0.314, 1.0] |
| Ne | Color |
Set the color for the element Ne | [0.702, 0.89, 0.961, 1.0] |
| Na | Color |
Set the color for the element Na | [0.671, 0.361, 0.949, 1.0] |
| Mg | Color |
Set the color for the element Mg | [0.541, 1.0, 0.0, 1.0] |
| Al | Color |
Set the color for the element Al | [0.749, 0.651, 0.651, 1.0] |
| Si | Color |
Set the color for the element Si | [0.941, 0.784, 0.627, 1.0] |
| P | Color |
Set the color for the element P | [1.0, 0.502, 0.0, 1.0] |
| S | Color |
Set the color for the element S | [1.0, 1.0, 0.188, 1.0] |
| Cl | Color |
Set the color for the element Cl | [0.122, 0.941, 0.122, 1.0] |
| Ar | Color |
Set the color for the element Ar | [0.502, 0.82, 0.89, 1.0] |
| K | Color |
Set the color for the element K | [0.561, 0.251, 0.831, 1.0] |
| Ca | Color |
Set the color for the element Ca | [0.239, 1.0, 0.0, 1.0] |
| Sc | Color |
Set the color for the element Sc | [0.902, 0.902, 0.902, 1.0] |
| Ti | Color |
Set the color for the element Ti | [0.749, 0.761, 0.78, 1.0] |
| V | Color |
Set the color for the element V | [0.651, 0.651, 0.671, 1.0] |
| Cr | Color |
Set the color for the element Cr | [0.541, 0.6, 0.78, 1.0] |
| Mn | Color |
Set the color for the element Mn | [0.612, 0.478, 0.78, 1.0] |
| Fe | Color |
Set the color for the element Fe | [0.878, 0.4, 0.2, 1.0] |
| Co | Color |
Set the color for the element Co | [1.0, 0.851, 0.561, 1.0] |
| Ni | Color |
Set the color for the element Ni | [0.78, 0.541, 0.541, 1.0] |
| Cu | Color |
Set the color for the element Cu | [0.784, 0.502, 0.2, 1.0] |
| Zn | Color |
Set the color for the element Zn | [0.49, 0.502, 0.69, 1.0] |
| Ga | Color |
Set the color for the element Ga | [0.761, 0.561, 0.561, 1.0] |
| Ge | Color |
Set the color for the element Ge | [0.4, 0.561, 0.561, 1.0] |
| As | Color |
Set the color for the element As | [0.741, 0.502, 0.89, 1.0] |
| Se | Color |
Set the color for the element Se | [1.0, 0.631, 0.0, 1.0] |
| Br | Color |
Set the color for the element Br | [0.651, 0.161, 0.161, 1.0] |
| Kr | Color |
Set the color for the element Kr | [0.361, 0.722, 0.82, 1.0] |
| Rb | Color |
Set the color for the element Rb | [0.439, 0.18, 0.69, 1.0] |
| Sr | Color |
Set the color for the element Sr | [0.0, 1.0, 0.0, 1.0] |
| Y | Color |
Set the color for the element Y | [0.58, 1.0, 1.0, 1.0] |
| Zr | Color |
Set the color for the element Zr | [0.58, 0.878, 0.878, 1.0] |
| Nb | Color |
Set the color for the element Nb | [0.451, 0.761, 0.788, 1.0] |
| Mo | Color |
Set the color for the element Mo | [0.329, 0.71, 0.71, 1.0] |
| Tc | Color |
Set the color for the element Tc | [0.231, 0.62, 0.62, 1.0] |
| Ru | Color |
Set the color for the element Ru | [0.141, 0.49, 0.49, 1.0] |
| Rh | Color |
Set the color for the element Rh | [0.039, 0.49, 0.549, 1.0] |
| Pd | Color |
Set the color for the element Pd | [0.0, 0.412, 0.522, 1.0] |
| Ag | Color |
Set the color for the element Ag | [0.753, 0.753, 0.753, 1.0] |
| Cd | Color |
Set the color for the element Cd | [1.0, 0.851, 0.561, 1.0] |
| In | Color |
Set the color for the element In | [0.651, 0.459, 0.451, 1.0] |
| Sn | Color |
Set the color for the element Sn | [0.4, 0.502, 0.502, 1.0] |
| Sb | Color |
Set the color for the element Sb | [0.62, 0.388, 0.71, 1.0] |
| Te | Color |
Set the color for the element Te | [0.831, 0.478, 0.0, 1.0] |
| I | Color |
Set the color for the element I | [0.58, 0.0, 0.58, 1.0] |
| Xe | Color |
Set the color for the element Xe | [0.259, 0.62, 0.69, 1.0] |
| Cs | Color |
Set the color for the element Cs | [0.341, 0.09, 0.561, 1.0] |
| Ba | Color |
Set the color for the element Ba | [0.0, 0.788, 0.0, 1.0] |
| La | Color |
Set the color for the element La | [0.439, 0.831, 1.0, 1.0] |
| Ce | Color |
Set the color for the element Ce | [1.0, 1.0, 0.78, 1.0] |
| Pr | Color |
Set the color for the element Pr | [0.851, 1.0, 0.78, 1.0] |
| Nd | Color |
Set the color for the element Nd | [0.78, 1.0, 0.78, 1.0] |
| Pm | Color |
Set the color for the element Pm | [0.639, 1.0, 0.78, 1.0] |
| Sm | Color |
Set the color for the element Sm | [0.561, 1.0, 0.78, 1.0] |
| Eu | Color |
Set the color for the element Eu | [0.38, 1.0, 0.78, 1.0] |
| Gd | Color |
Set the color for the element Gd | [0.271, 1.0, 0.78, 1.0] |
| Tb | Color |
Set the color for the element Tb | [0.188, 1.0, 0.78, 1.0] |
| Dy | Color |
Set the color for the element Dy | [0.122, 1.0, 0.78, 1.0] |
| Ho | Color |
Set the color for the element Ho | [0.0, 1.0, 0.612, 1.0] |
| Er | Color |
Set the color for the element Er | [0.0, 0.902, 0.459, 1.0] |
| Tm | Color |
Set the color for the element Tm | [0.0, 0.831, 0.322, 1.0] |
| Yb | Color |
Set the color for the element Yb | [0.0, 0.749, 0.22, 1.0] |
| Lu | Color |
Set the color for the element Lu | [0.0, 0.671, 0.141, 1.0] |
| Hf | Color |
Set the color for the element Hf | [0.302, 0.761, 1.0, 1.0] |
| Ta | Color |
Set the color for the element Ta | [0.302, 0.651, 1.0, 1.0] |
| W | Color |
Set the color for the element W | [0.129, 0.58, 0.839, 1.0] |
| Re | Color |
Set the color for the element Re | [0.149, 0.49, 0.671, 1.0] |
| Os | Color |
Set the color for the element Os | [0.149, 0.4, 0.588, 1.0] |
| Ir | Color |
Set the color for the element Ir | [0.09, 0.329, 0.529, 1.0] |
| Pt | Color |
Set the color for the element Pt | [0.816, 0.816, 0.878, 1.0] |
| Au | Color |
Set the color for the element Au | [1.0, 0.82, 0.137, 1.0] |
| Hg | Color |
Set the color for the element Hg | [0.722, 0.722, 0.816, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
[0.0, 0.0, 0.0, 1.0] |
Color Atomic Number
Choose the color for an individual atomic_number. Useful for joining with fields and selecting individual elements for coloring
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| atomic_number | Int |
The atomic_number of to use the selected color for |
None |
| Color | Color |
The color to use for the specified atomic_number |
[0.8, 0.8, 0.8, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The generated color based on the node inputs | [0.0, 0.0, 0.0, 0.0] |
Color Res Name
Choose colors for the individual amino acid and nucleic acid residues
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| ALA | Color |
Set the color for the residue ALA | [0.0, 0.0, 0.0, 1.0] |
| ARG | Color |
Set the color for the residue ARG | [0.095, 0.095, 0.095, 1.0] |
| ASN | Color |
Set the color for the residue ASN | [0.114, 0.22, 0.185, 1.0] |
| ASP | Color |
Set the color for the residue ASP | [0.141, 0.337, 0.429, 1.0] |
| CYS | Color |
Set the color for the residue CYS | [0.281, 0.151, 0.106, 1.0] |
| GLU | Color |
Set the color for the residue GLU | [0.202, 0.202, 0.202, 1.0] |
| GLN | Color |
Set the color for the residue GLN | [0.128, 0.205, 0.8, 1.0] |
| GLY | Color |
Set the color for the residue GLY | [0.8, 0.069, 0.068, 1.0] |
| HIS | Color |
Set the color for the residue HIS | [0.184, 0.761, 0.341, 1.0] |
| ILE | Color |
Set the color for the residue ILE | [0.091, 0.627, 0.129, 1.0] |
| LEU | Color |
Set the color for the residue LEU | [0.037, 0.17, 0.411, 1.0] |
| LYS | Color |
Set the color for the residue LYS | [0.052, 0.052, 0.052, 1.0] |
| MET | Color |
Set the color for the residue MET | [0.528, 0.452, 0.498, 1.0] |
| PHE | Color |
Set the color for the residue PHE | [0.359, 0.305, 0.094, 1.0] |
| PRO | Color |
Set the color for the residue PRO | [0.8, 0.172, 0.525, 1.0] |
| SER | Color |
Set the color for the residue SER | [0.8, 0.722, 0.052, 1.0] |
| THR | Color |
Set the color for the residue THR | [0.106, 1.0, 0.116, 1.0] |
| TRP | Color |
Set the color for the residue TRP | [0.528, 0.137, 0.411, 1.0] |
| TYR | Color |
Set the color for the residue TYR | [0.086, 0.365, 0.638, 1.0] |
| VAL | Color |
Set the color for the residue VAL | [0.069, 0.152, 0.56, 1.0] |
| A | Color |
Set the color for the residue A | [0.274, 0.548, 0.8, 1.0] |
| C | Color |
Set the color for the residue C | [0.295, 0.8, 0.188, 1.0] |
| G | Color |
Set the color for the residue G | [0.85, 0.251, 0.178, 1.0] |
| T | Color |
Set the color for the residue T | [0.8, 0.27, 0.527, 1.0] |
| rA | Color |
Set the color for the residue rA | [0.274, 0.548, 0.8, 1.0] |
| rC | Color |
Set the color for the residue rC | [0.295, 0.8, 0.188, 1.0] |
| rG | Color |
Set the color for the residue rG | [0.85, 0.251, 0.178, 1.0] |
| rU | Color |
Set the color for the residue rU | [0.8, 0.27, 0.527, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
[0.8, 0.8, 0.8, 1.0] |
Color Common
For convenience, choose colors for the common 6 elements found protein structures
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Hydrogen | Color |
Color to set for the element Hydrogen | [1.0, 1.0, 1.0, 1.0] |
| Carbon | Color |
Color to set for the element Carbon | [0.202, 0.202, 0.202, 1.0] |
| Nitrogen | Color |
Color to set for the element Nitrogen | [0.16, 0.233, 0.8, 1.0] |
| Oxygen | Color |
Color to set for the element Oxygen | [0.8, 0.161, 0.16, 1.0] |
| Phosphorous | Color |
Color to set for the element Phosphorous | [0.8, 0.172, 0.525, 1.0] |
| Sulfur | Color |
Color to set for the element Sulfur | [0.8, 0.722, 0.052, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The output colors for the common elements | [0.0, 0.0, 0.0, 0.0] |
Color Goodsell
Darken the color of non-carbon atoms, a similar strategy to the style developed by David Goodsell
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Invert | Bool |
Whether to invert the darkening of the colors | False |
| Factor | Float |
Amount to apply the ‘Goodsell Style’ coloring to | 0.5 |
| Color | Color |
Color to apply ‘Goodsell’ style colors to | [0.5, 0.5, 0.5, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The generated color based on the node inputs | [0.0, 0.0, 0.0, 0.0] |
Color Rainbow
Output a rainbow color spectrum along the structure. The rainbow can be generated along each chain in the structure, or along the entire structure. You can offset the strat of the rainbow and chain the color & satuation of the generated colors
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Per Chain | Bool |
Generate a rainbow that starts and stops for each individual chain | False |
| Offset | Float |
Offset rainbow along chain | 0.0 |
| Color Saturation | Float |
The Saturation value of the rainbow colors |
0.8 |
| Color Value | Float |
The Value value of the resulting rainbow colors |
0.8 |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The generated color | [0.8, 0.8, 0.8, 1.0] |
Color Attribute Map
Map a value to interpolate between two colors, optionally using an intermediate color. User can specify the Attribute Name that is used for the inerpolation, specifying the start and end values of the interpolation
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Attribute Name | String |
Name of the attribute to map colors to | b_factor |
| Attribute Min | Float |
Value for the attribute to be the minimum color | 0.0 |
| Attribute Max | Float |
Value for the attribute to be the maxium color | 150.0 |
| Color Use Mid | Bool |
Wheter to interpolate through the ‘Mid’ color. | True |
| Color Min | Color |
Color mapped to the minimum value of the attribute | [0.077, 0.479, 0.5, 1.0] |
| Color Mid | Color |
Color mapped to the middle value of the attribute | [0.5, 0.5, 0.5, 1.0] |
| Color Max | Color |
Color mapped to the maximum value of the attribute | [0.5, 0.159, 0.058, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The mapped color value based on the attribute. | [0.0, 0.0, 0.0, 0.0] |
Color Attribute Random
Generate a random color, based on the given attribute. Control the lightness and saturation of the color with the inputs.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Name | String |
Attribute to base the random color generation on | chain_id |
| Color Saturation | Float |
Saturlation level for the random color | 0.6 |
| Color Lightness | Float |
Lightness value for the generated random color | 0.6 |
| Color Seed | Int |
Seed value for the random generation of the colors | None |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The randomly generated color based on the input attribute | [0.0, 0.0, 0.0, 0.0] |
Color pLDDT
Uses the b_factor attribute to assign the typical AlphaFold pLDDT color palette. Node is automatically used when fetching directly from the AlphaFold database
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| <50 | Color |
Color for pLDTT < 50 | [1.0, 0.205, 0.06, 1.0] |
| <70 | Color |
Color for 50 < pLDTT < 70 | [1.0, 0.708, 0.007, 1.0] |
| <90 | Color |
Color for 70 < pLDTT < 90 | [0.13, 0.597, 0.896, 1.0] |
| >90 | Color |
Color for 90 < pLDTT | [0.0, 0.086, 0.672, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
Assigned color based on the pLDTT score | [0.0, 0.0, 0.0, 0.0] |
Color Backbone
Select colors for atoms that are part of the backbone or the side chain of a peptide or nucleic acid polymer. Atoms that are neither maintain their current Color attribute
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Backbone | Color |
[0.469, 0.24, 0.6, 1.0] |
|
| Side Chain | Color |
[0.526, 0.6, 0.24, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
[0.0, 0.0, 0.0, 0.0] |
Color Sec Struct
Choose a color for the different secondary structures, based on the sec_struct attribute.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
| Alpha Helix | Color |
Color to set for alpha helices | [0.162, 0.624, 0.195, 1.0] |
| Beta Sheet | Color |
Color to set for beta-sheets | [1.0, 0.15, 0.15, 1.0] |
| Loop | Color |
Color to set for loops in the structure | [0.171, 0.366, 0.799, 1.0] |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
| Color | Color |
The colors based on secondary structure | [0.0, 0.0, 0.0, 0.0] |