[Chimera-users] delete atoms based on their coordinates

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 17 15:45:07 PDT 2014

Hi Michelle,
Zones are defined based on distance from existing atom(s) rather than a point in space.  The fudgy user-interface way to do it would be to create a dummy atom at (x,y,z) and then delete it and all the other atoms in the desired annihilation zone.

(1) Create dummy atom. menu:  Tools… Structure Editing… Build Structure, section: Start Structure, option Add: atom with specified x,y,z coordinates.  Add the atom to the same model that has your other atoms to make sure they are in the same coordinate system.
(2) Delete dummy atom along with its zone.  You could use the option in Start Structure to select the new atom upon its creation, then menu: Select… Zone, then Actions… Atoms/Bonds… delete, or a command, e.g.

delete sel za<5.5


delete sel z<5.5

(z specifies the whole residues with any atom within the zone, za specifies just the atoms within the zone).  Or if the dummy weren't selected, the default added atom is element He, so you could just substitute "He" for "sel" in the example commands above.

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 Jun 17, 2014, at 2:22 PM, "Aranha, Michelle" <maranha at vols.utk.edu> wrote:

> Hi ,
> I wanted to know if there is a way in chimera to select and delete atom/atoms based on their position/coordinates in the simulation box. For example delete water 150 at (x, y, z). I tried zone sel, but I couldnt get it to work.
> Regards,
> Michelle

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