Coloring

You can choose to color the sequences by a wide range of attributes. First, you can choose what you want to color by choosing Apply to All, Group, or Marked. Then, you can choose the coloring method that you wish to apply. In VMD in Graphics $\rightarrow$ Colors in the color scale tab you can choose the overall color scale for VMD such as RWB and RGB⁷. Also, Multiseq can display a color scale for you based on the coloring method selected in VMD(see 9.5).

Add current Selection colors all selected molecules

Alignment Position colors the sequences based on length where the begining, middle and end of a sequence will have different colors

Contact colors the sequence based on the number of contacts or the order of contacts

Insertions takes the first structure in multiseq and colors sequence insertions based on that sequence

Mutual Information takes 2 or more align groups and colors them based on mutually shared identities

$Q_{res}$ aka Q per residue colors the sequence based on the contribution from each residue to the overall average Q score. For more information see 10.3.

Residue Type Colors amino acid residues by whether they are acidic or basic.

RMSD takes aligned sequences and colors based on the distanced between two $C^{\alpha}$ of aligned residues

Sequence Conservation colors residues based on their conservation with all other sequences in Multiseq

Sequence Entropy colors columns of sequences based on the conservation of sequence

Sequence Identity method colors each amino acid according to the degree of conservation within the alignment: blue means highly conserved, wheras red means very low or no conservation in the default RWB color setting.

Sequence Similarity colors aligned sequences based on BLOSUM or a custom subsitution matrix

Signatures colors sequences based on sequence signatures. These options include: Minimum fraction conserved to be a group signature:, Maximum fraction of signatures allowed in other groups:, Maximum fraction of gaps allowed in other groups:, Maximum distance of signature from a conserved block:, Minimum length of conserved block:

Custom is a way to import custom tcl scripts with specific coloring commands

Import allows you to import color dat files that had been previously exported using Export Data

Refresh Color is used if you believe that your newest color change was not implemented