Hi Francesco, You would have to use residue numbers and/or chain IDs. Actually the peptide is also "protein" (at least the standard residues) so you would not want to use that specifier anyway. If your peptide was chain B and the protein was chain C, for example: sel :.c & :.b z<5 Or if everything was chain A and your protein is residue numbers 3-455 and the peptide is residues number 456-462: sel :3-455.a & :456-462.a z<5 There are several ways to figure out the numbers and chain IDs, including looking at the balloon help that pops up when you hold the cursor over some atoms on the screen, or using the Sequence tool, or using a text-editor to look at the PDB file. See "atom specification" for details on using model, residue, chain IDs etc. in the command line. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
Best, 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 Sep 12, 2010, at 7:28 AM, Francesco Pietra wrote:
Hello: How to map the residues at a given distance (<5A) between a protein and its 5-residues peptide ligand? I could only use the zone command for a non-standard residue in the peptide:
sel protein & :non-standard_residuename_of_peptide
All other peptide residues are standard residues.
thanks francesco pietra