Hi Francesco, Maybe I misunderstood your question. At first I thought you wanted all residues in one structure within some distance of *specific* residues in another. However, maybe you meant you would just like to know all the residue-residue contacts between two structures. In that case, just use the Find Clashes/Contacts tool (or the command "findclash"). These can write out a list of all the contacting atom pairs, their VDW overlaps (which could be negative where the atoms are not touching), and distances. Depending on how you set the cutoffs, you can list only very close contacts ("clashes") or also include atom pairs that are farther apart. Besides cutoffs, there are several other options such as saving to a file, drawing lines to show the contacts, etc. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> for example: open 1zik findclash :.a log true checks for clashes between chain A and all other atoms, and sends the following information to the Reply Log: 4 contacts atom1 atom2 overlap distance LEU 5.A CD1 MET 2.B CE 0.769 2.991 MET 2.A CE MET 2.B CE 0.761 2.999 MET 2.A CA MET 2.B CE 0.707 3.053 VAL 23.A CG2 VAL 23.B CG2 0.707 3.053 In your example, you could just open your two models and specify #0 to find all the contacts between #0 and everything else. If you use the GUI instead of the command, you would select all atoms of #0 and "Designate" them for checking against all other atoms. This tutorial includes use of Find Clashes/Contacts: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> - the "Distances, H-Bonds Contacts" part uses the tool to identify binding site residues, and then does some other stuff to write out a list of the residues instead of atom pairs - the "Angles, Rotamers, Clashes" part uses the tool to identify clashes while rotating a side chain interactively I hope this helps, 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 Oct 8, 2008, at 10:23 AM, Francesco Pietra wrote:

What I would like to do is a global search of which residues of model #0 are within a certain distance from which residues of model #1. Where "model" stands for a protein in both cases. That would save time in simulations of docking (not using DOCK) between proteins. I can locate with Chimera key residues, but their number is large. Thanks francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users