From: Jérôme Hénin (
Date: Mon Dec 13 2021 - 09:42:33 CST


What file format are you saving the coordinates in?


----- On 13 Déc 21, at 15:46, Liel Sapir <> wrote:

> Hello,
> I am trying to use vmd to edit a coordinate file but removing some atoms. My
> problem is that once I save the new coordinates to a new file all the atom
> indices are automatically reassigned. Is there a way to avoid this within vmd?

> Thank you,

> Liel