[Chimera-users] R: Removing specific water molecules

Francesca Magarotto - francesca.magarotto2@studio.unibo.it francesca.magarotto2 at studio.unibo.it
Thu Jun 10 08:16:46 PDT 2021

The first option worked,
thank you really much for your help.
Da: Elaine Meng <meng at cgl.ucsf.edu>
Inviato: giovedì 10 giugno 2021 17:09
A: Francesca Magarotto - francesca.magarotto2 at studio.unibo.it <francesca.magarotto2 at studio.unibo.it>
Cc: Chimera-users at cgl.ucsf.edu <Chimera-users at cgl.ucsf.edu>
Oggetto: Re: [Chimera-users] Removing specific water molecules

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 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 at 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

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