[Chimera-users] sequence viewer

mgochin at touro.edu mgochin at touro.edu
Thu Dec 18 10:31:41 PST 2008

I have to agree that I much prefer the old sequence viewer.

- Miriam

---- Original message ----
>Date: Thu, 18 Dec 2008 10:20:07 -0800
>From: Eric Pettersen <pett at cgl.ucsf.edu>  
>Subject: Re: [Chimera-users] sequence viewer  
>To: "Gatsogiannis, Christos" <gatsogia at uni-mainz.de>
>Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
>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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