From: Alexander Adams (
Date: Thu May 26 2022 - 17:50:41 CDT

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.


University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering