Frank von Delft wrote:
> I can't help thinking I saw this recently, yet I can't find it:
Ah... the power of jiscmail's search...?
>
> Is there a script command that will align two chains by SSM, but
> taking into account only a subset of residues from each? (E.g. if I
> want to compare relative domain orientations of distant homologues, I
> want to align only one domain from each homologue.)
Yes.
http://www.ysbl.york.ac.uk/~emsley/coot/doc/doxygen/html/c-interface_8h.html#a892
>
> And relatedly: what's the scheme command for SSM? I didn't spot it in
> the manual, although that could have been just me being crap.
>
It is in the manual - but hiding a bit, perhaps:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_4.html#SEC86
It is indeed related.
I'd imagine that you want something like
(superpose-with-atom-selection 0 1 "A/22-220" "B/33-330" 0)
Paul.
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