On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote:

Hi all, I am trying to find all the atoms that lie within a certain distance from a selected chains. I am able to do this by going to select -> zone and giving the distance I want and selecting all the atoms that met my criteria. I would like to do this on command line. I am unable to figure it out. Any help would be greatly appreciated. Thank You Thiru Ramaraj

Hi Thiru, The following command would select all residues with any atom within 4.5 angstroms of your current selection: select sel z<4.5 You could use "za" instead of "z" if you want an atom-based cutoff instead of whole residues, > instead of < to get the atoms farther away, and of course, a different distance. Also, you don't have to use selections. For example, this would color all atoms within 5 angstroms of chain A red: color red :.a za<5 Description of command-line zone specification: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ atom_spec.html#zones> More examples appear in various tutorials: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ attributes.html#part2> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ squalene.html#surfaces> 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