Hi Francesco, You can write out a list of what is selected with "Actions... Write List" or the coordinates of the selected atoms as a PDB file with "Actions... Write PDB". The dialog for writing a list lets you choose whether you want atoms or just residues listed, and the style to use, as explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec There are several features (and corresponding parts of the documentation) that relate to RMSD. If you choose "Help... Search Documentation" from the menu and search for "rmsd" you get a list. From your description, you probably want to use the command "rmsd" - it calculates RMSD between two sets of atoms without moving/fitting them. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html Other things that relate to RMSD (see documentation if you need more details): - the "match" command, which fits the two specified sets of atoms and then reports the resulting RMSD - "matchmaker" command or MatchMaker tool, superimposes proteins and reports alpha-carbon RMSD for the residue pairs used in the fit - EnsembleMatch tool, which calculates all pairwise RMSD values for specified atoms within an ensemble of structures that contain identical atoms - MD Movie tool, which can calculate all pairwise RMSD values for selected atoms within frames of a trajectory I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 13, 2007, at 7:49 AM, Francesco Pietra wrote:

I am looking at the protein residues "responsible" for docking a single-residue ligand.

select protein & :ligandname z<#

works for various values of #. I would like to print the list of residues instead of having to detect them from the screen, which may lead to errors.

Also, which section of the manual concerns RMSD? (I would like to calculate RMSD at various stages of DOCK6.1 and Amber9 MD for the above, i..e. how the ligand adapts and the protein follows it, or vice-versa).

Thanks francesco pietra