[Chimera-users] shape sphere

[Elaine Meng]

Hi Francesco,
Shape sphere does not help with the task you describe.  Instead just use a zone specification.  If the atom you want to use as the center is selected, for example to delete all atoms farther away from it than 25 angstroms:

delete sel za>25

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>

There is no “undo” for this except reopening the structure, so make sure you have a saved copy before deleting.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 20, 2019, at 7:55 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> I have read the manual about shape sphere. What I would like to do is retaining all proteic, nucleosidic, organic ligands, ions and water molecules that exist within a sphere of, say, 25A centered at a certain atom of a ligand, while discarding everything outside the sphere.
> Because of the content, are there special flags to be used?
> 
> thanks
> francesco pietra
> (actually I am already trying with general commands but python is already working from 1 and 1/2 hr without any outcome)d