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!