Residue Letter Coloring

The Clustal X coloring scheme in Multalign Viewer depends on both residue type and the pattern of conservation within a column. The Clustal X scheme is described in the color parameter file colprot.par. This scheme is encoded in Chimera and cannot be changed by users.

However, arbitrary color schemes can be defined using the same file format and loaded with File... Load Color Scheme in the Multalign Viewer menu. When a scheme is loaded, the residue codes are colored accordingly and the name of the custom coloring file is added to the list of choices for Residue letter coloring in the Analysis preferences. The dialog for loading the file includes an option to Make this scheme the default. The location of each custom coloring file is saved in the preferences file. If a custom coloring file is later renamed, moved, or deleted, trying to load the corresponding scheme will generate an error.

Multalign Viewer uses the same format of color parameter file as the program Clustal X. Examples:

• colprot.par (describes Clustal X residue letter coloring)
• custom.par (an example of custom coloring; matches the protein structure coloring done with the Chimera command file rescol.com)

1. Colors are defined in the optional @rgbindex section. If the section is present, it must include all of the colors used in the file. Each line in this section consists of a color name and the red, green, and blue components of the color, for example:

   GREEN        0.1 0.8 0.1
   

   The color names are relevant only to the rules within the file; for example, GREEN as defined in this file cannot be accessed by Chimera users and can differ from the color named green in Chimera.
   
   
2. The @consensus section assigns single-character symbols to column consensus conditions. The symbols can be uppercase or lowercase letters, which should not be confused with the single-letter residue codes (although they are sometimes the same for mnemonic reasons). For example,

   + = 60% k:r
   

   means that "+" symbolizes the case where lysine and arginine together comprise at least 60% of the column of aligned amino acids, and

   n = 50% n
   N = 85% n
   

   means that "n" symbolizes the case where asparagine comprises at least 50% of the column and "N" symbolizes the case where asparagine comprises at least 85% of the column.
   
   
3. The @color section then assigns colors to particular residues under particular consensus conditions. Thus,

   n = GREEN if n:N:D
   

   means that an asparagine in the alignment (which could be shown with n or N) should be colored GREEN if any of the conditions n, N, or D apply to the column in which it resides. When none of the conditions apply, the residue is colored black.