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Molecular Visualization by Color

Coloring molecular structures uses various schemes to highlight components and features. With Copilot, you can easily apply these techniques, simplifying visualization and analysis. Examples of coloring methods are provided in the following sections to enhance clarity.

Color by secondary structure

Color by plddt

Color Molecules by Their Atomic Chemical Elements:

This method colors atoms according to standard conventions: C is gray, O is red, N is blue, H is white, and S is yellow, among others.

Color Proteins by Their Secondary Structure:

This technique applies distinct colors to represent different secondary structures, such as helices, sheets, turns, and more.

Color Molecules by Residue Name:

This method assigns a unique color to each residue name, allowing for easy differentiation between them.

Color Molecules by b-Factor Values:

This technique applies a gradient based on the b-factor column to visualize variations in atomic displacement.

Color Molecules by pLDDT Score:

This method uses a color scale to represent confidence levels: very low is orange, low is yellow, high is cyan, and very high is blue, assuming the b-factor column contains pLDDT values.

  • By Name: Red, blue, peach, moonlight green, ...
  • Custom: #78FF00, #0078FF, ...