I know you can get alignments from Chimera - pre-superimposed output
is from the Match > Align menu
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
Alignment gives backbone RMSD as well.
I have only used this for pairwise alignments but the documentation
shows three superimiposed and aligned.
hope that helps.
Martyn
Cambridge
On Thu, Dec 3, 2015 at 4:23 PM, Natalia O <[log in to unmask]> wrote:
> Dear All,
>
> I apologize for an off topic question. I was told that if I have several
> structures aligned structurally elsewhere (not in pymol), then if I open all
> these coordinates in pymol I can retrieve a sequence alignment based on the
> structural alignment.
> I guess more broadly I am trying to figure out how to get a sequence
> alignment that represents structural alignment. I know ways to do it one by
> one, but I wonder if there is an efficient way to do it for many structures
> that are already structurally aligned?
>
> Thank you a lot!
> Yours,
> Natalia
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