[chimera-dev] Feature request

David E. Konerding dakone at uclink.berkeley.edu
Tue Sep 10 11:59:06 PDT 2002

Eric Pettersen wrote:

> Hi David,
>     We will be discussing this at an upcoming Chimera meeting.  There 
> are several possible ways to implement what you want, including a 
> "show sequence" column in the model panel, a "sequences" panel under 
> the Controllers menu, or a "sequences" rollover menu in the 
> Controllers menu to get to particular models/chains.  We were hoping 
> you could describe your workflow with respect to the sequence panel so 
> we could get some idea what would work out and what won't 
> (particularly in respect to whether you need sequences from multiple 
> models displayed simultaneously -- or whether being able to flip 
> between sequences quickly would be adequate).

I want to be able see and interact with sequences from multiple models 

Basically, the work I'm doing for CASP, which I will be working on even 
more now that I'm moving to Brenner's
lab, involves dealing with many multiple sequence alignments where 
(some) sequences map to structures.  The problem
is that sometimes due to the database being searched, the sequence 
contains residues which are not present
in the PDB file due to missing atom records.  So, I have to spend a lot 
of time looking at structure, looking at sequence,
and looking at alignments, to map the residue ranges properly.  

The latter two suggestions (sequences panel that lets me see all 
unaligned sequences) and sequences rollover menu (I assume
this is a dynamically generated submenu in the menu list for 
'Controllers') are nice.  I want both :-)

What would be *really really* great is being able to mouse-over residues 
in the sequence panel and see a corresponding
highlight (a small enclosing box around the residue, for example) in the 
MAV alignment, and to be able to select residues in the sequence panel and
see them highlighted in the alignment.  Alternatively, it almost seems 
as if the sequence panel is *redundant* in that the alignment viewer
could also act as a sequence panel, which would simply things-- could 
the alignment viewer be modified to be an "unalignment viewer"?



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