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

Sabuj Pattanayek sabuj.pattanayek at vanderbilt.edu
Fri Jul 29 10:58:37 PDT 2005


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)?

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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