Clustal X 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. In brief, a Clustal X color parameter file has three sections:

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.