[Chimera-users] Structure to sequence alignment

Elaine Meng meng at cgl.ucsf.edu
Fri May 28 08:44:53 PDT 2021

Hi Kamil,
I don't understand the "color corresponding residues" and "colored as mutually corresponding" part, so maybe Chimera does not have that.

However, in Chimera you can 
- display multiple protein structures as CA traces
- display the protein sequences together in a sequence alignment window
- edit the sequence alignment

First open all the structures and then hide ribbons and show chain trace, for example commands:

chain @ca

One way to to get the sequence alignment is to use Matchmaker (menu: Tools... Structure Comparison... Matchmaker) to first superimpose all the structures in 3D, and then use Match->Align (in same part of menu as Matchmaker) to create a multiple sequence alignment based on their 3D alignment. 

... see also tutorial:

Or if you already have a sequence alignment file of those sequences created in some other program, you could just open it in Chimera.  Here are the sequence formats Chimera can read:

Then if you want to improve the sequence alignment, you can use sequence-window menu: Edit... Realign Sequences, and/or you can manually edit the sequences.  (You can also realign the structures in 3D using the sequence alignment.)

You can see what parts of sequence are what parts of structure by selecting in one, which will automatically show as green highlights on the other.

HOWEVER, although Chimera allows manual editing of the sequence alignment, it is not very easy.  If you need to do a lot of editing, it may be better in another program such as Jalview.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 28, 2021, at 12:44 AM, Kamil Steczkiewicz <kamil.steczkiewicz at gmail.com> wrote:
> Dear Chimera community,
> Does Chimera allow to display multiple protein structures as CA trace, colour corresponding residues in 3d, display these proteins' sequences in alignment window and allow to manually alter the alignment to manually align residues coloured as mutually corresponding (preferably by mouse)? Something like was possible in good old and unfortunately not supported any more Insight program... That's what wraps up to so-called structure-based manual multiple sequence alignment. Essential if you're assessing some highly diversified set of structures and want to have a precise alignment for them.
> Thanks,
> Kamil

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