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

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 2 11:32:23 PDT 2014

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 Pettersen
                        UCSF Computer Graphics Lab

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