[Chimera-users] zone

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 10 20:13:16 PST 2011

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.


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):

I hope this helps,
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

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