[Chimera-users] Need Information

[Elaine Meng]

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/cxcolor.html>

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/multalignviewer.html#mavpref-layout>

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 at 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