Hi Jean-Paul, Maybe I'm misunderstanding your question, but you can use the standard command-line zone specifiers za (atom-based cutoff) and zr (same as z, residue-based cutoff, which gets whole residue even if only one of its atoms is within the cutoff). These have been available in Chimera for several years. Examples: show #1 & #0 z<5 - display only the atoms of residues in model 1 that have any atom within 5 angstroms of model 0. Commands show and display only control atoms/bonds, you may also want to do a similar thing with ribbons, for example, if the whole ribbon is already shown: ~ribbon #1 & #0 z>5 - to hide ribbon of residues in model 1 that don't have any atom within 5 angstroms of model 0. Many commands work with these zone specifiers, not just show/display, and the zone can be defined on any set of atoms, not necessarily a whole model. Another example: color red ligand za<4.7 (color atoms in all models red that are within 4.7 angstroms of residues classified as "ligand") Information on command-line atom specification (see "Zones" section): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 10, 2011, at 3:29 PM, Jean-Paul Armache wrote:

hello,

there is a zone function for density maps+pdbs, which zones the map around the pdb in a certain radius. is it somehow feasible in chimera to do such thing with two pdbs ? what i mean is to zone a molecular model around another molecular model? (the reason for that is the speed, in which elaborate models are shown, sometimes zoning would be very useful for fast-checking). would be grateful for your help, best regards,

jean-paul