Hi Wisdom, The default residue letter coloring is "Clustal X", which depends on both residue type and the pattern of conservation within a column. Thus "R" could be different colors depending on what else is in the same column. The rules used by this coloring are contained in a parameter file, described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/cxc...> Although you can't change that parameter file, you can make and apply your own custom parameter file (as described in the link above), or simply choose a different coloring option in the Preferences (sequence window menu Preferences... Appearance). The options are described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mul...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 16, 2012, at 12:42 PM, wisdom@sanbi.ac.za wrote:
Hi, I am Wisdom, an MSc Bioinformatics student of the University of the Western Cape, South Africa. I wish to understand the meaning of the colouring of the individual amino acids in the sequence window of multiple sequence alignment as per the attached.
I one see that all the Rs indicated by the black arrow are all red while the blue arrow has black Rs and orange Gs in the same column. There are other similar coloring all over the alignment. What does each (green, black, blue, orange, purple,red ) colour represent? Thanks Wisdom