[Chimera-users] sequence viewer

Eric Pettersen pett at cgl.ucsf.edu
Thu Dec 18 10:20:07 PST 2008

Hi Christos,
	In previous releases, there were two tools that showed sequences:   
the sequence viewer (single sequences) and Multalign Viewer (sequence  
alignments).  We plan to show additional information with sequences  
(e.g. UniProt markups) and as a step in that direction we decided to  
unify our presentation of sequence info by making MAV capable of  
showing single sequences.  That way, the work to show sequence  
information in the user interface won't have to be duplicated each  
time we add something.
	So, rather than restore the old sequence viewer, what I would prefer  
to do is make the MAV interface better for showing single sequences.   
Would it help if single sequences were combined in a single dialog,  
like in the previous sequence viewer?  I don't think that's too hard  
to do.  As for color, I think you're right that for a single sequence  
it makes more sense to show that columns as black, since there is no  
conservation per se down the column.  I can easily change that.  You  
can too, in fact, by choosing Preferences->Analysis in the MAV window  
and changing "Residue letter coloring" to "black" (the preference will  
be carried over to future MAV dialogs).
	So what other changes would make the MAV version of the sequence  
version more usable?  I guess this is actually a general question to  


On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:

> Hi all,
> i ve just installed the latest daily build version and i´ve noticed  
> that the sequence viewer has a new "look".
> However, i have difficulties to get used to it...
> Some examples:
> -when i want to view the sequence of a pdb file containing seven  
> chains, i get seven different pop-up windows (...) showing the   
> sequences corresponding to the seven different chain ID´s....
> -Moreover, it isn´t so "easy" anymore to select  aminoacids directly  
> in the sequence viewer (e.g. too many colors) and therefore now i´m  
> selecting residues using only the command line..
> My colleagues also prefer the older version..
> is there a simple way to install the latest chimera version but keep  
> the old version of the sequence viewer?
> Thanks!

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