[Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 18 11:34:39 PST 2015

On Feb 18, 2015, at 7:39 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier.

Making it easier to add conservation/consensus lines that apply to only subsets of sequences would indeed be pretty useful.  It's actually already on my "to do" list (#12388 (allow conservation to be shown for sequence subsets)), but many things on my to-do list haven't been getting the attention I'd like as we work hard to try to get "Chimera 2" at least minimally up and running.  Sort of as a corollary, this will probably get implemented in Chimera 2 rather than Chimera 1, which as you can imagine means it will be awhile before it sees the light of day.  So for now you are going to have to use the less nice workarounds you are currently using to get your work done.  I'm sorry about that.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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