From: John Stone (
Date: Wed Nov 07 2018 - 14:30:01 CST

  Yes, you can create an empty molecule using "mol new atoms xxx",
and then use atom selection commands to assign all of their properties.
When finished, you can then issue a "mol reanalyze" command so that
VMD will honor all of the new properties and assignments you have made.
This is in fact the low level mechanism used by a few of the structure
preparation tools, including the "toopotools" plugin, for example.

  John Stone

On Wed, Nov 07, 2018 at 08:45:21PM +0100, Michail Lazaratos wrote:
> Greetings VMD users,
> i want to create new atoms in VMD as a part of a visualization.
> So far i can create atoms with the command "mol new atoms 1".
> Is is possible to assign resnames, resids, segnames and most importantly
> coordinates to those new atoms.
> If you have any suggestions let me know.
> Thank you in advance,
> Michail Lazaratos

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349