[Chimera-users] rmsd overlay

[Francesco Pietra]

Elaine:

> If you are only superimposing one pair of atoms (one atom in one model,
> another in a different model), an easy way is to just select the two atoms
> (ctrl-click, Shift-ctrl-click) and then use command: match sel
>

That worked nicely, the fake atom brought all its connections with. I had
only to combine the generated models (on saving pdb), deleting the original
metal atoms.

Thanks
francesco

On Mon, Oct 12, 2015 at 9:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> You would use the “match” command.  The atoms don’t need to have the same
> names since they are specified in the command.  Of course, if you are
> matching fewer than 3 pairs of atoms, the superposition will not be
> unique.  It will still work, but there will be a warning.
>
> If you are only superimposing one pair of atoms (one atom in one model,
> another in a different model), an easy way is to just select the two atoms
> (ctrl-click, Shift-ctrl-click) and then use command: match sel
>
> That will move the model containing the atom you selected first.
> Otherwise you could specify atoms in the normal command-line way by model
> number, residue number or name, chain ID, and atom name.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic
> >
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Oct 12, 2015, at 10:12 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >
> > Hello;
> >
> > Ho to superimpose a fake atom (pdb file available) to a coordiated metal
> in a protein? I could change the name of the fake atom to that of the
> metal, but then I need an rmsd overlay.
> >
> > hope it is clear. thanks
> >
> > francesco pietra
>
>
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