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

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 29 11:50:57 PDT 2005

Hi Sabuj,
     Multalign Viewer should be able to read either SCF format.  Let  
me know if it doesn't.
     You can hack your Chimera distribution to get the behavior you  
asked for originally without too much effort.  The Multalign Viewer  
source is in <your installation>/share/MultAlignViewer.  You will  
need to change the files Consensus.py and SeqCanvas.py.  In  
Consensus, change the value of capitalizeAt from 0.8 to 1.1 (never  
produce capital letters).  In the evaluate() method, move:

             if num == len(self.seqs):
                 self.conserved[pos] = 1

out of the surrounding 'if' (which is now never true).  In SeqCanvas,  
in the layout() method there is a colorConsensus() embedded  
function.  Remove the test for uppercase characters and reverse the  
logic so that it returns 'red' for unconserved and 'black' otherwise.
     I should offer better control over consensus properties,  
especially now that I am working on supporting phylogenetic trees and  
will be showing consensus/conservation lines for subtrees.  Another  
related thing I'm working on is supporting Python plugins that add  
header lines that not only depict characters (in various colors) but  
simple shapes such as rectangles, circles, arrows, etc.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Jul 29, 2005, at 10:58 AM, Sabuj Pattanayek wrote:

> Hi,
> Thanks for mentioning the SCF file. I can create a script to create  
> the file from the alignment. Does the SCF parser in the multialign  
> viewer read the new format or the old format (I guess newer)?
> Thanks,
> Sabuj Pattanayek
> Elaine Meng wrote:
>>> 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
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