[Chimera-users] Structure to sequence alignment

[Kamil Steczkiewicz]

Elaine,
I really appreciate your detailed answer. I will go through multiple
options and try to figure out how to do the alignment.
Best,
Kamil

pt., 28 maj 2021 o 17:44 Elaine Meng <meng at cgl.ucsf.edu> napisał(a):

> 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:
>
> ~ribbon
> 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.
>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
> >
> ... see also tutorial:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
> >
>
> 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:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment
> >
>
> 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.)
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
> >
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing
> >
>
> 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.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#crosstalk
> >
>
> 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
> -----
> 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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