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)
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@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
participants (2)
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Elaine Meng -
Francesco Pietra