Hi Jean-Paul, The possibilities I have in mind are not particularly "automatic": (a) use multiple "distance" commands, each specifying a pair of atoms. You would probably want to write a script in your favorite language to create the Chimera command file with all those distance commands. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/distance.html

(b) use the "findclash" command (or GUI) with an extremely lenient cutoff (large negative overlap), which will report all the distances within that cutoff. Specify finding interactions between your one residue and all other atoms to get the distances and overlaps for all atom-atom pairs meeting the criteria. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html

<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/f...

With (b) you would get a lot of output to sift through. If you wanted only certain atoms, for example CA-CA distances only, you would either just use approach (a) or use (b) with postprocessing to extract only the lines of interest. 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 Mar 31, 2009, at 5:17 AM, Jean-Paul Armache wrote:

hello, i would like to ask whether there is a way of automatically measuring the distance from all residues in a chain to residue X in the same chain? best regards, jean-paul armache