From: Axel Kohlmeyer (
Date: Fri Dec 12 2014 - 05:20:29 CST

On Thu, Dec 11, 2014 at 5:43 PM, Eric Smoll <> wrote:
> Hello vmd users,
> When a file is loaded with "mol new $filename" in a tcl script, is this
> molecule visible to atomselect expressions in a procedure? If not, what is
> the recommended way to "pass" or "make visible" the molecule in the local
> scope of a function?

molecules are a global property and thus always visible.
when you create a new molecule, the return value of the mol command is
the molecule id of the new molecule, so you can do something like

set mol [mol new $filename]
set sel [atomselect $mol all]


> Best,
> Eric

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.