Hi Francesca,
I can't say for certain without having your exact PDB file to test, but some things to try would be

delete solvent & :546-893
- or -
delete :546-893.water

How these water residues are written (and thus how to specify them) depends on the program that made the file.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 10, 2021, at 7:47 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi,
> I have a problem using Chimera: I need to delete specific water molecules with a specific residue number, but this number is in common with residues that are useful (such as ligands or co-factors).
> For example, I type "del :546-893" in the command line in order to delete these water molecules, but I delete also the ligand and FAD and I don't want to.
> I've read the guide about atom specification, but still I don't know how to do it.
> Hope someone can help me,
> thank you.
> Francesca