[Chimera-users] coloring of nearly identical protein sequences in multialign viewer

[Elaine Meng]

> Hi all,
>
> I have a clustal aln file or a fasta file with two nearly identical  
> aligned protein sequences. When I view them in the multialign  
> viewer I would like to change the color of the consensus style.  
> That is, residues which are both identical should be just black  
> (rather than red and capitalized) and residues that are not  
> identical should be red (or some other color that contrasts against  
> black). Is there anyway to do this?
>
> Better yet would it be possible to not use the consensus at all and  
> color the entire non-matching column a color of my choice?
>
> Thanks,
> Sabuj Pattanayek

Hi Sabuj,
Currently there is no way to change the Consensus line contents from  
the user interface. All you can do is to turn it off entirely (from  
the Multalign Viewer window, Preferences... Analysis and set the  
"Consensus style" to "none").  If your alignment just has two  
sequences, however, all the columns where there is no bar in the  
Conservation histogram when the "Conservation style" is set to  
"identity histogram," or no asterisk when the "Conservation style" is  
set to "Clustal characters" are those in which the two sequences  
differ.  That is the closest I can get to your request,  
unfortunately.  There is a format of input that lets you color rows  
and columns in the alignment, but then you'd have to calculate  
yourself which positions had differing residues and then write out  
such a file.  Maybe too bothersome to be worth it.  Such a file is  
loaded into Multalign Viewer using "Tools... Load SCF/Seqsel File"  
and the file format is described in:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
multalignviewer/jevtrace.html

Coming soon:  we just added more and fancier options for  
"Conservation style" which, although they do not address your  
specific question in this mail, might interest you:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
multalignviewer/multalignviewer.html#mavpref-analysis

(development documentation; we don't have a release with these  
features yet)
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html