From: Ashar Malik (
Date: Thu Dec 11 2014 - 18:01:48 CST

Depends how you do it. When a molecule is loaded its assigned an ID. You
could also pass the "top" to the atomselect, depends on what you have.

Also to directly answer your question ... When you load it, it becomes
available, as long as its loaded in the visualizer. You have to make a call
to in your script.


atomselect top all

Will select everything in your molecule.

Hope this answers your question.

On Dec 12, 2014 12:06 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?
> Best,
> Eric