From: Abhijit Muley (
Date: Wed Aug 20 2014 - 09:09:27 CDT

Hi Albert,

You can use Tk console and do the following:

set sel [atomselect top "ligand or (water and within 4 of ligand)"]
$sel writepdb sel.pdb

(You have to replace ligand and water with appropriate keywords).

mol new sel.pdb

You have now loaded the ligand with water molecules within 4 angstroms


On Wed, Aug 20, 2014 at 2:59 PM, Albert <> wrote:

> Hello:
> I am going to delete water molecule within 4 A around a ligand. Every time
> I have to do this from GUI: save the whole system excluding 4A water
> molecules within ligand.
> I am just wondering, can we do it from command line?
> thank you very much.
> Albert