Hi Francesco, Maybe I am misunderstanding the question, but why not just select a zone around the ligand (with a command or "Select... Zone" in the menu), or use Find Clashes/Contacts (or the findclash command) to select residues in contact with the ligand? <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuselect> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> This is nearly the same topic as discussed last month in "pruning PDB": <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003183.html

... you could write out a list of the selected residues (Actions... Write List or writesel command), undisplay the other residues, etc. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html> The "Structural Analysis and Comparison" tutorial (Distances, H-Bonds, Contacts section) includes an example of using Find Clashes/Contacts to write a list of the residues in a ligand-binding site: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#dist...

Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 12, 2008, at 8:43 AM, Francesco Pietra wrote:

A polypeptide was docked onto a protein that already carried ligands. Then, molecular dynamics of the complex was carried out. To do this, a single PDB file was created with the program ptraj of Amber.

Although ptraj removes chain labels, TER lines, etc., renumbering all the residues in a single sequence, I know, from the ligand positions, the corresponding numbering for the chains and for the polypeptide.

Which is the best procedure to map around certain groups of amino acids of the protein, i.e., those that constitute the experimentally-evaluated binding site? I want to take notice of which residues of the polypeptide are most involved in the binding.

Thanks

francesco pietra