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