[Chimera-users] sequence viewer
pett at cgl.ucsf.edu
Mon Jul 13 16:43:42 PDT 2009
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.
UCSF Computer Graphics Lab
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
> 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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> Chimera-users at cgl.ucsf.edu
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