[Chimera-users] Analysis of the multiple alignments + structures

James Starlight jmsstarlight at gmail.com
Wed Sep 3 05:11:45 PDT 2014

Thank you very much for suggestions!
Regarding techniqal question: Indeed I've found that the JalView + Chimera
Mutalign give me best results! ;)

Elaine, how do you think might the *selective* analysis of the alignments
of *different* branches of the phylogenetic tree of the olfactory receptors
be more effective for the the prediction of the mutations affecting its
specifity and affinity towards different clases of ligands (odors)? I've
noticed that the same aproach have been used in your 2003 study
(Evolutionary trace of GPCRs) where you made conclusions (mainly based on
the  selectivy analys of the Opsins) about mutations affecting i) ligand
binding site, iii) constitutive activity as well as ii) coupling to the

Kind regards,


2014-09-02 22:32 GMT+04:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> On Sep 2, 2014, at 10:53 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Some teqnichal question: is it possible in Chimera (using mut align plugin
> for instance)  to redunce number of sequences ussed in the  conservation
> diagrams as well as in the in multiple alignments diagrams (for inctance to
> hide some sequences from the all set which will not been used)?  E.g:
> Previously I've had to make new aligmnet.fasta files with different number
> of sequences and load it each time in the Chimera when I need to compare
> different number of sequences. But in fact I'd like to do it within one
> open Chimera session with the set of maximum number of sequences hidding
> the unused sequences.
> What Elaine said about there being no percent-ID filtering is correct,
> nonetheless there are a couple of tips here for working with a subset of
> sequences.  You can drag out a region on the main alignment that covers the
> sequences you are interested and then directly create an alignment from
> them with the Edit/Region->New Window menu item.  If you have trouble with
> that (I did for one specific alignment file and will be fixing the problem
> after I send this mail!) you can also use File/Save As to save the region
> to a file (make sure to click the "Restrict save to active region" button
> on the Save As dialog) and then open that file.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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