Hi,
I'd say that align would be a good start with a selection like:
align byres protein1 within 5 of metalion1, byres protein2 within 5 of
metalion2
And from there you can see if further refinement is needed. The 5A is
arbitrary :p
Cheers,
Tsjerk
On Sat, Nov 9, 2013 at 1:24 PM, Mike Marchywka <marchy...@hotmail.com>wrote:
> ________________________________
> > From: ccp4...@hotmail.com
> > To: pymol-users@lists.sourceforge.net
> > Date: Fri, 8 Nov 2013 19:53:50 -0600
> > Subject: [PyMOL] alignment of metal coordination
> >
> > Hi,
> >
> > Is it possible to align two structure based on metal coordination or
> > metal-coordinating residues? What is good way to do it?
>
> Is this a 1-D alignment or spatial ? There are conserved sequence DB's
> and of course if you want to check there are things like citeseer and
> pubmed
> as well as google scholar for finding algorithms if nothing exists in
> pymol.
>
> Maybe someone can comment on how to do this in pymol but
> you can always define your own figure of merit and optimize that as a
> function
> of relative orientation. I suppose you can define an ordering of residues
> based on
> interactions with metals. I actually downloaded several orderings from
> ( hotmail makes it almost impossible any more to insert links into plain
> text messages....
> now thinking I must mean html )
>
> http://www.expasy.org/tools/protscale.html\
>
> for exampl,e,
> Hphob.Argos.tr KDRENQPHYSWTGCAVMILF
>
>
>
> > I appreciate your guidance.
> >
> > Thanks
> > SDY
> >
> >
> >
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--
Tsjerk A. Wassenaar, Ph.D.
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