Color
Set Color
The is the primary way to change the color of structures in Molecular Nodes. Colors for cartoon and ribbon are taken from the alpha-carbons of the structures. Change the color of the input atoms, based on a selection and a color field. The color field can be as complex of a calculation as you wish. In the example below the color for the whole structure can be set, or the color can be based on a color for each chain, or the result of mapping a color to an attribute such as b_factor.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Atoms |
Geometry | Atomic geometry that contains vertices and edges | required |
Selection |
Bool | Selection of atoms to apply this node to | True |
Color |
Color | Color to apply to the selected atoms | rgb(41, 159, 49)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Atoms |
Geometry | Atomic geometry with an updated Color attribute |
required |
Chain
Choose the colors for individual chains in the structure. This node is generated for each particular molecule, so the inputs will look different based on the imported structure. For larger structures with many chains this node may become too large to be practical, in which case you might better use Color Entity ID.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Chain A |
Color | Color to set for Chain A | rgb(117, 153, 61)◉ |
Chain B |
Color | Color to set for Chain B | rgb(61, 153, 146)◉ |
... |
Color | Color to set for Chain … | rgb(153, 61, 118)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The colors based on chain_id |
rgb(0, 0, 0)◉ |
Segment
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Segment A |
Color | Color to set for Ligand B | rgb(117, 153, 61)◉ |
Segment B |
Color | Color to set for Ligand B | rgb(61, 153, 146)◉ |
... |
Color | Color to set for Ligand … | rgb(153, 61, 118)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The colors based on entity_id |
rgb(0, 0, 0)◉ |
Entity
Choose the colors for individual entities in the structure. Multiple chains may be classified as the same entity, if they are copies of the same chain but in different conformations or positions and rotations. The nodes is generated for each individual structure, if entity_id is available.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Entity A |
Color | Color to set for Entity A | rgb(117, 153, 61)◉ |
Entity B |
Color | Color to set for Entity B | rgb(61, 153, 146)◉ |
... |
Color | Color to set for Entity … | rgb(153, 61, 118)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The colors based on entity_id |
rgb(0, 0, 0)◉ |
Ligand
Choose the colors for individual ligands in the structure.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Ligand A |
Color | Color to set for Ligand B | rgb(117, 153, 61)◉ |
Ligand B |
Color | Color to set for Ligand B | rgb(61, 153, 146)◉ |
... |
Color | Color to set for Ligand … | rgb(153, 61, 118)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The colors based on entity_id |
rgb(0, 0, 0)◉ |
Element
Choose a color for each of the first 20 elements on the periodic table. For higher atomic number elements use Color Atomic Number.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
H |
Color | rgb(255, 255, 255)◉ |
|
He |
Color | rgb(217, 255, 255)◉ |
|
Li |
Color | rgb(204, 128, 255)◉ |
|
Be |
Color | rgb(194, 255, 0)◉ |
|
B |
Color | rgb(255, 181, 181)◉ |
|
C |
Color | rgb(144, 144, 144)◉ |
|
N |
Color | rgb(48, 80, 248)◉ |
|
O |
Color | rgb(255, 13, 13)◉ |
|
F |
Color | rgb(144, 224, 80)◉ |
|
Ne |
Color | rgb(179, 227, 245)◉ |
|
Na |
Color | rgb(171, 92, 242)◉ |
|
Mg |
Color | rgb(138, 255, 0)◉ |
|
Al |
Color | rgb(191, 166, 166)◉ |
|
Si |
Color | rgb(240, 200, 160)◉ |
|
P |
Color | rgb(255, 128, 0)◉ |
|
S |
Color | rgb(255, 255, 48)◉ |
|
Cl |
Color | rgb(31, 240, 31)◉ |
|
Ar |
Color | rgb(128, 209, 227)◉ |
|
K |
Color | rgb(143, 64, 212)◉ |
|
Ca |
Color | rgb(61, 255, 0)◉ |
|
Sc |
Color | rgb(230, 230, 230)◉ |
|
Ti |
Color | rgb(191, 194, 199)◉ |
|
V |
Color | rgb(166, 166, 171)◉ |
|
Cr |
Color | rgb(138, 153, 199)◉ |
|
Mn |
Color | rgb(156, 122, 199)◉ |
|
Fe |
Color | rgb(224, 102, 51)◉ |
|
Co |
Color | rgb(255, 217, 143)◉ |
|
Ni |
Color | rgb(199, 138, 138)◉ |
|
Cu |
Color | rgb(200, 128, 51)◉ |
|
Zn |
Color | rgb(125, 128, 176)◉ |
|
Ga |
Color | rgb(194, 143, 143)◉ |
|
Ge |
Color | rgb(102, 143, 143)◉ |
|
As |
Color | rgb(189, 128, 227)◉ |
|
Se |
Color | rgb(255, 161, 0)◉ |
|
Br |
Color | rgb(166, 41, 41)◉ |
|
Kr |
Color | rgb(92, 184, 209)◉ |
|
Rb |
Color | rgb(112, 46, 176)◉ |
|
Sr |
Color | rgb(0, 255, 0)◉ |
|
Y |
Color | rgb(148, 255, 255)◉ |
|
Zr |
Color | rgb(148, 224, 224)◉ |
|
Nb |
Color | rgb(115, 194, 201)◉ |
|
Mo |
Color | rgb(84, 181, 181)◉ |
|
Tc |
Color | rgb(59, 158, 158)◉ |
|
Ru |
Color | rgb(36, 125, 125)◉ |
|
Rh |
Color | rgb(10, 125, 140)◉ |
|
Pd |
Color | rgb(0, 105, 133)◉ |
|
Ag |
Color | rgb(192, 192, 192)◉ |
|
Cd |
Color | rgb(255, 217, 143)◉ |
|
In |
Color | rgb(166, 117, 115)◉ |
|
Sn |
Color | rgb(102, 128, 128)◉ |
|
Sb |
Color | rgb(158, 99, 181)◉ |
|
Te |
Color | rgb(212, 122, 0)◉ |
|
I |
Color | rgb(148, 0, 148)◉ |
|
Xe |
Color | rgb(66, 158, 176)◉ |
|
Cs |
Color | rgb(87, 23, 143)◉ |
|
Ba |
Color | rgb(0, 201, 0)◉ |
|
La |
Color | rgb(112, 212, 255)◉ |
|
Ce |
Color | rgb(255, 255, 199)◉ |
|
Pr |
Color | rgb(217, 255, 199)◉ |
|
Nd |
Color | rgb(199, 255, 199)◉ |
|
Pm |
Color | rgb(163, 255, 199)◉ |
|
Sm |
Color | rgb(143, 255, 199)◉ |
|
Eu |
Color | rgb(97, 255, 199)◉ |
|
Gd |
Color | rgb(69, 255, 199)◉ |
|
Tb |
Color | rgb(48, 255, 199)◉ |
|
Dy |
Color | rgb(31, 255, 199)◉ |
|
Ho |
Color | rgb(0, 255, 156)◉ |
|
Er |
Color | rgb(0, 230, 117)◉ |
|
Tm |
Color | rgb(0, 212, 82)◉ |
|
Yb |
Color | rgb(0, 191, 56)◉ |
|
Lu |
Color | rgb(0, 171, 36)◉ |
|
Hf |
Color | rgb(77, 194, 255)◉ |
|
Ta |
Color | rgb(77, 166, 255)◉ |
|
W |
Color | rgb(33, 148, 214)◉ |
|
Re |
Color | rgb(38, 125, 171)◉ |
|
Os |
Color | rgb(38, 102, 150)◉ |
|
Ir |
Color | rgb(23, 84, 135)◉ |
|
Pt |
Color | rgb(208, 208, 224)◉ |
|
Au |
Color | rgb(255, 209, 35)◉ |
|
Hg |
Color | rgb(184, 184, 208)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(0, 0, 0)◉ |
Atomic Number
Choose a color for an individual element. Select the element based on atomic_number. Useful for higher atomic number elements which are less commonly found in structures.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
atomic_number |
Int | 6 |
|
Color |
Color | rgb(204, 204, 204)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(0, 0, 0)◉ |
Res Name
Choose a color for each of the 20 naturally occurring amino acids or the 4 base nucleic acids (DNA / RNA)
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
ALA |
Color | rgb(0, 0, 0)◉ |
|
ARG |
Color | rgb(24, 24, 24)◉ |
|
ASN |
Color | rgb(29, 56, 47)◉ |
|
ASP |
Color | rgb(35, 86, 109)◉ |
|
CYS |
Color | rgb(71, 38, 26)◉ |
|
GLU |
Color | rgb(51, 51, 51)◉ |
|
GLN |
Color | rgb(32, 52, 204)◉ |
|
GLY |
Color | rgb(204, 17, 17)◉ |
|
HIS |
Color | rgb(46, 194, 86)◉ |
|
ILE |
Color | rgb(23, 159, 33)◉ |
|
LEU |
Color | rgb(9, 43, 104)◉ |
|
LYS |
Color | rgb(13, 13, 13)◉ |
|
MET |
Color | rgb(134, 115, 126)◉ |
|
PHE |
Color | rgb(91, 77, 24)◉ |
|
PRO |
Color | rgb(204, 43, 133)◉ |
|
SER |
Color | rgb(204, 184, 13)◉ |
|
THR |
Color | rgb(27, 255, 29)◉ |
|
TRP |
Color | rgb(134, 34, 104)◉ |
|
TYR |
Color | rgb(21, 93, 162)◉ |
|
VAL |
Color | rgb(17, 38, 142)◉ |
|
A |
Color | rgb(69, 139, 204)◉ |
|
C |
Color | rgb(75, 204, 47)◉ |
|
G |
Color | rgb(216, 64, 45)◉ |
|
T |
Color | rgb(204, 68, 134)◉ |
|
rA |
Color | rgb(69, 139, 204)◉ |
|
rC |
Color | rgb(75, 204, 47)◉ |
|
rG |
Color | rgb(216, 64, 45)◉ |
|
rU |
Color | rgb(204, 68, 134)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(204, 204, 204)◉ |
Common Elements
Choose a color for each of the common elements. This is a smaller convenience node for elements which commonly appear in macromolecular structures
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Hydrogen |
Color | Color to set for the element Hydrogen | rgb(255, 255, 255)◉ |
Carbon |
Color | Color to set for the element Carbon | rgb(51, 51, 51)◉ |
Nitrogen |
Color | Color to set for the element Nitrogen | rgb(40, 59, 204)◉ |
Oxygen |
Color | Color to set for the element Oxygen | rgb(204, 41, 40)◉ |
Phosphorous |
Color | Color to set for the element Phosphorous | rgb(204, 43, 133)◉ |
Sulfur |
Color | Color to set for the element Sulfur | rgb(204, 184, 13)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The output colors for the common elements | rgb(0, 0, 0)◉ |
Goodsell
Change the inputted color to be darker for non-carbon atoms. Creates a Goodsell Style color scheme for individual chains.
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 | rgb(127, 127, 127)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(0, 0, 0)◉ |
Rainbow
Generate a rainbow color palette, that changes over from start to finish along a peptide chain. Can be one rainbow over the entire structure, or create a rainbow of a per-chani basis.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Per Chain |
Bool | False |
|
Offset |
Float | Offset rainbow along chain | 0.0 |
Color Saturation |
Float | 0.8 |
|
Color Value |
Float | 0.8 |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(204, 204, 204)◉ |
Attribute Map
Interpolate between two or three colors, based on the value of an attribute field such as b_factor. Choosing the minimum and maximum values with the inputs.
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 | rgb(19, 122, 127)◉ |
Color Mid |
Color | Color mapped to the middle value of the attribute | rgb(127, 127, 127)◉ |
Color Max |
Color | Color mapped t othe maximum value of the attribute | rgb(127, 40, 14)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The mapped color value based on the attribute. | rgb(0, 0, 0)◉ |
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 | 0 |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The randomly generated color based on the input attribute | rgb(0, 0, 0)◉ |
pLDDT
Assigns colors using the b_factor attribute, which contains the pLDDT attribute for models that come from AlphaFold.
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
<50 |
Color | Color for pLDTT < 50 | rgb(255, 52, 15)◉ |
<70 |
Color | Color for 50 < pLDTT < 70 | rgb(255, 180, 1)◉ |
<90 |
Color | Color for 70 < pLDTT < 90 | rgb(33, 152, 228)◉ |
>90 |
Color | Color for 90 < pLDTT | rgb(0, 22, 171)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | Assigned color based on the pLDTT score | rgb(0, 0, 0)◉ |
Backbone
Color atoms by whether or not they form part of a peptide or nucleic backbone
Inputs
| Name | Type | Description | Default |
|---|---|---|---|
Backbone |
Color | rgb(119, 61, 153)◉ |
|
Side Chain |
Color | rgb(134, 153, 61)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | rgb(0, 0, 0)◉ |
Secondary Structure
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 | rgb(41, 159, 49)◉ |
Beta Sheet |
Color | Color to set for beta-sheets | rgb(255, 38, 38)◉ |
Loop |
Color | Color to set for loops | rgb(43, 93, 203)◉ |
Outputs
| Name | Type | Description | Default |
|---|---|---|---|
Color |
Color | The colors based on secondary structure | rgb(0, 0, 0)◉ |