Color Sequences Pane Features

• Color schemes & settings section
  • Reset link
  • Apply to option menu
  • Color by option menu
  • Weight Colors by Alignment Quality option
  • Average Colors in Columns option
• Highlight selected residues section
  • Clear All Highlights
  • Paint Selected color palette
  • Outline Selected blocks color palette
• Color structures in Workspace section
  • Apply colors to Workspace options
  • Color Carbons button

Color schemes & settings section

Choose the color scheme and the target residues. If sequences are of a different type from the reference sequence (e.g. nucleic acids vs proteins), the color scheme for the sequence types that differ are faded, to highlight the different type.

Reset link

Reset the color scheme settings to the default values.

Apply to option menu

Choose the set of residues to apply the color to.

• All residues on tab—color all residues on the tab
• Residues matching reference—color only the residues in the other sequences that match the reference (identities)
• Residues differing from reference—color only the residues in the other sequences that do not match the reference
• Residues matching consensus—color only the residues that match the consensus sequence in all sequences
• Residues differing from consensus—color only the residues that do not match the consensus sequence in all sequences
• No residues—do not color any residues. This is equivalent to turning off coloring.

If sequences have a different type from the reference, they are not colored at all for the choices involving the reference.

Color by option menu and information button

Choose the color scheme to apply to the set of residues. Clicking the information button to the right of the menu shows a legend for the color scheme.

• Side Chain Chemistry—Color the residues by the side-chain chemistry, according to the following scheme.

  Scheme	Residues	Color	Description
  DE	red	acidic, hydrophilic
  HKR	blue	basic, hydrophilic
  AGILMV	green	neutral, hydrophobic, aliphatic
  FWY	orange	neutral, hydrophobic, aromatic
  NSTQ	cyan	neutral, hydrophilic
  C	yellow	primary thiol
  P	dark gray	imino acid

• Residue type—Color the residues by residue type. The colors are:

  ACFILMPVW	blue	(hydrophobic)
  DE	red	(acidic)
  HKR	green-yellow	(basic)
  GNQSTY	orange	(other)

• Residue similarity—Color residues by similarity. Identical residues are red, similar residues (positive BLOSUM62 pairwise score) are orange, other residues are white.

• Hydrophobicity (Kyte-Doolittle)—Color residues by Kyte-Doolittle hydrophobicity. Hydrophilic residues are blue, hydrophobic residues are red, residues with zero hydrophobicity are white.

• Hydrophobicity (Hopp-Woods)—Color residues by Hopp-Woods hydrophilicity. Hydrophilic residues are red, hydrophobic residues are blue, residues with zero hydrophobicity are white.

• Taylor scheme—Color residues with the Aminochromography color scheme developed by William Taylor (Protein Engineering 1997, 10, 743–746). In this scheme, well conserved parts of the alignment exhibit bright, clear colors, while parts that are not well conserved have brownish, dull colors.

• Clustal X Scheme—Scheme used for results of ClustalW program. See Clustal X Colour Scheme for the definition.

• Secondary Structure—Color the residues by the secondary structure assignment. If no SSA is available but one or more secondary structure predictions are available, the predictions are used to color the sequence. The colors for multiple predictions are averaged, so positions where all predictions agree have bright colors, and the positions of disagreement are more gray. If no SSP nor SSA is available, the color of the sequence is not changed.

• B-Factor—Color the residues by their temperature factor (PDB B factor), on a green-white-red scale, with green for the lowest values and red for the highest.

• Helix Propensity—color by propensity to form helices, according to the scheme below:

  Scheme	Residues	Color	Description
  AELKMQ	red	helix-forming
  IFVW	magenta	weak helix-forming
  CDHNRST	gray	ambivalent
  GPY	blue	helix-breaking

• Strand Propensity—color by propensity to form strands, according to the scheme below:

  Scheme	Residues	Color	Description
  FILMTVWY	blue	strand-forming
  ACHNQRS	gray	ambivalent
  DEGKP	red	strand-breaking

• Turn Propensity—color by propensity to form turns, according to the scheme below:

  Scheme	Residues	Color	Description
  DGNPS	cyan	turn-forming
  ACFHILMVW	magenta	turn-breaking
  EKQRTY	gray	ambivalent

• Exposure Tendency—color by tendency to solvent exposure, according to the scheme below:

  DEHKNQR	blue	surface
  ACGPSTWY	gray	ambiguous
  ILMFV	orange	buried

• Steric Group—color by the steric properties of the side chains, according to the scheme below:

  ACGS	red	small, noninterfering
  DILMNPTV	magenta	ambiguous
  EKQR	cyan	sticky polar
  FHWY	blue	aromatic

• Workspace Colors—color the sequences according to the color of the alpha carbon of the corresponding structure in the Workspace.

• Chain Name—color the sequence according to its chain name, with a different color for each (single-letter) name.

• Residue Position—colors the sequences by residue number. The first 10% (including the N-terminus) of the residues are red, the last 10% (C-terminus) are purple, and there is a rainbow color ramp between those ends.

• Residue Charge— color the sequences by residue charge. Positive residues are blue, negative residues are red, neutral residues are gray.

Weight Colors by Alignment Quality option

Adjust the color intensity according to the quality of the alignment.

Average Colors in Columns option

Average the colors in each column and display the average for each column.

Highlight selected residues section

Highlight the selected residues with a chosen color. This color overrides the current color scheme.

Clear All Highlights

Clear all highlighting of residues.

Paint Selected color palette

Color the selected residues with the color chosen from this palette. The "more" button opens a color selector to choose a custom color. The color is applied immediately.

Outline Selected blocks color palette

Create an outline around the selected residues with the color chosen from this palette.

Color structures in Workspace section

Color the structures in the Workspace.

Apply colors to Workspace options

Apply the colors to the Workspace structures as well as the sequences.

• Whenever they change—apply the new colors to the Workspace whenever the color scheme changes. The Color entire residues option is disabled, and the colors are applied to the current setting of this option.

• Color entire residues—Color the entire residue with the chosen color. The default is to color carbons only.

Color Carbons/Color Residues button

Apply the colors to the workspace according to the Color entire residues setting. The button changes when you select or deselect this setting.