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 simultaneously. 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"? :-) Dave