VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Fri Nov 11 2022 - 16:46:51 CST

Hi Caleb,

You are looking for "water and same residue as pbcwithin 3 of protein".

-Josh

On 11/11/22 3:51 PM, Huang, Caleb wrote:
> Hello,
>
> I am trying to select entire waters using pbwithin. This command --
> /set sel1 [atomselect top "water and pbwithin 3 of protein"] -- /will
> cut off atoms in a water molecule not within 3A (even if some within
> the molecule are). Is there any way I could select the entire water
> molecule if any atom within the water is within 3A of the protein?
>
> Thanks for any help!
> -Caleb
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io