VMD-L Mailing List

From: Alexander Adams (xadams_at_umich.edu)
Date: Thu May 26 2022 - 19:53:58 CDT

Hi John,

That fixed the problem. Thank you for the help.

Best,
Alex

On Thu, May 26, 2022 at 5:46 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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.
>
> Best,
> 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 EngineeringÂ
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
(he/him/his)
University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering