From: John Stone (
Date: Thu May 26 2022 - 19:46:00 CDT

Make sure to add "waitfor all" to the end of each of the "mol new" and
"mol addfile" commands so that they complete before the script is allowed
to continue.

  John Stone

On Thu, May 26, 2022 at 03:50:41PM -0700, Alexander Adams wrote:
> Dear VMD users,
> I've written a tcl script to align some ions to each of 3 protein chains
> and then save all of the ions as a merged file. The short story is that if
> I paste the script line by line into the Tkconsole it runs perfectly, but
> if I run via the command line (vmd -e align_coiledcoil_ions.tcl) it does
> not align properly. I was wondering if anyone had advice on what might be
> causing the problem, or how to diagnose it?
> For additional details, I've attached the script, and the specific problem
> is that only 1 of the 3 sets of ions align¬ properly and the other 2
> remain in the original position when I run it as a script instead of line
> by line. Please let me know¬ if I can provide additional information.
> Best,
> Alex
> --
> (he/him/his)
> University of Michigan, Ann Arbor
> Ph.D.¬ Candidate¬ -¬ Mayes Lab
> College of Engineering - Chemical Engineering¬

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