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	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

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	`[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 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	`[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 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	Default
H	`Color`	`[1.0, 1.0, 1.0, 1.0]`
He	`Color`	`[0.851, 1.0, 1.0, 1.0]`
Li	`Color`	`[0.8, 0.502, 1.0, 1.0]`
Be	`Color`	`[0.761, 1.0, 0.0, 1.0]`
B	`Color`	`[1.0, 0.71, 0.71, 1.0]`
C	`Color`	`[0.565, 0.565, 0.565, 1.0]`
N	`Color`	`[0.188, 0.314, 0.973, 1.0]`
O	`Color`	`[1.0, 0.051, 0.051, 1.0]`
F	`Color`	`[0.565, 0.878, 0.314, 1.0]`
Ne	`Color`	`[0.702, 0.89, 0.961, 1.0]`
Na	`Color`	`[0.671, 0.361, 0.949, 1.0]`
Mg	`Color`	`[0.541, 1.0, 0.0, 1.0]`
Al	`Color`	`[0.749, 0.651, 0.651, 1.0]`
Si	`Color`	`[0.941, 0.784, 0.627, 1.0]`
P	`Color`	`[1.0, 0.502, 0.0, 1.0]`
S	`Color`	`[1.0, 1.0, 0.188, 1.0]`
Cl	`Color`	`[0.122, 0.941, 0.122, 1.0]`
Ar	`Color`	`[0.502, 0.82, 0.89, 1.0]`
K	`Color`	`[0.561, 0.251, 0.831, 1.0]`
Ca	`Color`	`[0.239, 1.0, 0.0, 1.0]`
Sc	`Color`	`[0.902, 0.902, 0.902, 1.0]`
Ti	`Color`	`[0.749, 0.761, 0.78, 1.0]`
V	`Color`	`[0.651, 0.651, 0.671, 1.0]`
Cr	`Color`	`[0.541, 0.6, 0.78, 1.0]`
Mn	`Color`	`[0.612, 0.478, 0.78, 1.0]`
Fe	`Color`	`[0.878, 0.4, 0.2, 1.0]`
Co	`Color`	`[1.0, 0.851, 0.561, 1.0]`
Ni	`Color`	`[0.78, 0.541, 0.541, 1.0]`
Cu	`Color`	`[0.784, 0.502, 0.2, 1.0]`
Zn	`Color`	`[0.49, 0.502, 0.69, 1.0]`
Ga	`Color`	`[0.761, 0.561, 0.561, 1.0]`
Ge	`Color`	`[0.4, 0.561, 0.561, 1.0]`
As	`Color`	`[0.741, 0.502, 0.89, 1.0]`
Se	`Color`	`[1.0, 0.631, 0.0, 1.0]`
Br	`Color`	`[0.651, 0.161, 0.161, 1.0]`
Kr	`Color`	`[0.361, 0.722, 0.82, 1.0]`
Rb	`Color`	`[0.439, 0.18, 0.69, 1.0]`
Sr	`Color`	`[0.0, 1.0, 0.0, 1.0]`
Y	`Color`	`[0.58, 1.0, 1.0, 1.0]`
Zr	`Color`	`[0.58, 0.878, 0.878, 1.0]`
Nb	`Color`	`[0.451, 0.761, 0.788, 1.0]`
Mo	`Color`	`[0.329, 0.71, 0.71, 1.0]`
Tc	`Color`	`[0.231, 0.62, 0.62, 1.0]`
Ru	`Color`	`[0.141, 0.49, 0.49, 1.0]`
Rh	`Color`	`[0.039, 0.49, 0.549, 1.0]`
Pd	`Color`	`[0.0, 0.412, 0.522, 1.0]`
Ag	`Color`	`[0.753, 0.753, 0.753, 1.0]`
Cd	`Color`	`[1.0, 0.851, 0.561, 1.0]`
In	`Color`	`[0.651, 0.459, 0.451, 1.0]`
Sn	`Color`	`[0.4, 0.502, 0.502, 1.0]`
Sb	`Color`	`[0.62, 0.388, 0.71, 1.0]`
Te	`Color`	`[0.831, 0.478, 0.0, 1.0]`
I	`Color`	`[0.58, 0.0, 0.58, 1.0]`
Xe	`Color`	`[0.259, 0.62, 0.69, 1.0]`
Cs	`Color`	`[0.341, 0.09, 0.561, 1.0]`
Ba	`Color`	`[0.0, 0.788, 0.0, 1.0]`
La	`Color`	`[0.439, 0.831, 1.0, 1.0]`
Ce	`Color`	`[1.0, 1.0, 0.78, 1.0]`
Pr	`Color`	`[0.851, 1.0, 0.78, 1.0]`
Nd	`Color`	`[0.78, 1.0, 0.78, 1.0]`
Pm	`Color`	`[0.639, 1.0, 0.78, 1.0]`
Sm	`Color`	`[0.561, 1.0, 0.78, 1.0]`
Eu	`Color`	`[0.38, 1.0, 0.78, 1.0]`
Gd	`Color`	`[0.271, 1.0, 0.78, 1.0]`
Tb	`Color`	`[0.188, 1.0, 0.78, 1.0]`
Dy	`Color`	`[0.122, 1.0, 0.78, 1.0]`
Ho	`Color`	`[0.0, 1.0, 0.612, 1.0]`
Er	`Color`	`[0.0, 0.902, 0.459, 1.0]`
Tm	`Color`	`[0.0, 0.831, 0.322, 1.0]`
Yb	`Color`	`[0.0, 0.749, 0.22, 1.0]`
Lu	`Color`	`[0.0, 0.671, 0.141, 1.0]`
Hf	`Color`	`[0.302, 0.761, 1.0, 1.0]`
Ta	`Color`	`[0.302, 0.651, 1.0, 1.0]`
W	`Color`	`[0.129, 0.58, 0.839, 1.0]`
Re	`Color`	`[0.149, 0.49, 0.671, 1.0]`
Os	`Color`	`[0.149, 0.4, 0.588, 1.0]`
Ir	`Color`	`[0.09, 0.329, 0.529, 1.0]`
Pt	`Color`	`[0.816, 0.816, 0.878, 1.0]`
Au	`Color`	`[1.0, 0.82, 0.137, 1.0]`
Hg	`Color`	`[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 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`		None
Color	`Color`		`[0.8, 0.8, 0.8, 1.0]`

Outputs

Name	Type	Description	Default
Color	`Color`		`[0.0, 0.0, 0.0, 0.0]`

Color 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	Default
ALA	`Color`	`[0.0, 0.0, 0.0, 1.0]`
ARG	`Color`	`[0.095, 0.095, 0.095, 1.0]`
ASN	`Color`	`[0.114, 0.22, 0.185, 1.0]`
ASP	`Color`	`[0.141, 0.337, 0.429, 1.0]`
CYS	`Color`	`[0.281, 0.151, 0.106, 1.0]`
GLU	`Color`	`[0.202, 0.202, 0.202, 1.0]`
GLN	`Color`	`[0.128, 0.205, 0.8, 1.0]`
GLY	`Color`	`[0.8, 0.069, 0.068, 1.0]`
HIS	`Color`	`[0.184, 0.761, 0.341, 1.0]`
ILE	`Color`	`[0.091, 0.627, 0.129, 1.0]`
LEU	`Color`	`[0.037, 0.17, 0.411, 1.0]`
LYS	`Color`	`[0.052, 0.052, 0.052, 1.0]`
MET	`Color`	`[0.528, 0.452, 0.498, 1.0]`
PHE	`Color`	`[0.359, 0.305, 0.094, 1.0]`
PRO	`Color`	`[0.8, 0.172, 0.525, 1.0]`
SER	`Color`	`[0.8, 0.722, 0.052, 1.0]`
THR	`Color`	`[0.106, 1.0, 0.116, 1.0]`
TRP	`Color`	`[0.528, 0.137, 0.411, 1.0]`
TYR	`Color`	`[0.086, 0.365, 0.638, 1.0]`
VAL	`Color`	`[0.069, 0.152, 0.56, 1.0]`
A	`Color`	`[0.274, 0.548, 0.8, 1.0]`
C	`Color`	`[0.295, 0.8, 0.188, 1.0]`
G	`Color`	`[0.85, 0.251, 0.178, 1.0]`
T	`Color`	`[0.8, 0.27, 0.527, 1.0]`
rA	`Color`	`[0.274, 0.548, 0.8, 1.0]`
rC	`Color`	`[0.295, 0.8, 0.188, 1.0]`
rG	`Color`	`[0.85, 0.251, 0.178, 1.0]`
rU	`Color`	`[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

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	`[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

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	`[0.5, 0.5, 0.5, 1.0]`

Outputs

Name	Type	Description	Default
Color	`Color`		`[0.0, 0.0, 0.0, 0.0]`

Color 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`		`[0.8, 0.8, 0.8, 1.0]`

Color 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	`[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 t othe 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

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	`[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

Color atoms by whether or not they form part of a peptide or nucleic backbone

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	`[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]`