Hi Yogendra, Yes, you can use any atoms that you want to superimpose two structures, as long as you can specify these atoms by residue name or number and atom name (if necessary), using the “match” command. You would not necessarily need to change their names unless that makes it easier to remember which atom should match each atom. There are example “match” commands in in the tutorials, for example the glycoside hydrolases image tutorial (go to the “matching” section): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> … and in the match manual page <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> How to specify residues/atoms in the command line: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Discussion of the different ways to match structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> 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 Dec 29, 2015, at 11:15 AM, Yogendra Ramtirtha <ramtirtha.yogendra@gmail.com> wrote:

I have to detect the presence of a ligand in many PDB files. So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand. Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ?

In general, can Chimera superimpose ligands in 2 PDB files ?

Thank you