[Chimera-users] sequence viewer

[Eric Pettersen]

Hi all,
	I have made my intended improvements to the single-sequence viewer  
now and the new version is in the daily build (which you can get by  
going to www.cgl.ucsf.edu/chimera and following the "Daily Builds"  
link).  I encourage people who use the sequence viewer a lot to fetch  
the new version and let me know what you like and what you don't.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Dec 18, 2008, at 10:20 AM, Eric Pettersen wrote:

> 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
> everybody...
>
> --Eric
>
> 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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