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
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
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
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Elaine Meng -
Francesco Pietra