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@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@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