[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.
---- 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>
> 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?
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