VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 02 2021 - 14:32:51 CST

Hi Phillip,
  We dug into the multiseq code today and indeed, there are some
issues with it's conficting use of both "grid" and "pack" GUI layout
managers that is almost certainly the cause of the hang you've seen.

One of my colleagues here has volunteered to make an attempt at
addressing these bugs since the original authors no longer
support the code. I'm hoping we can have relatively rapid turnaround
on a fix for this now that we've discovered some obvious underlying issues
that need to be corrected.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 01, 2021 at 12:42:12AM -0600, John Stone wrote:
> Hi,
> I'm guessing that this hang is caused by some bug in the multiseq
> plugin related to its use of Tk, but that is only a guess.
> Do you see any error messages in the main VMD console associated
> with the hanging behavior, or is the hang the only observable behavior?
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 26, 2021 at 11:05:02PM -0500, Phillip Compeau wrote:
> > Hi,
> >
> > I am integrating VMD into a publicly available assignment that I
> > provide to my course as well (https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
> > ).
> >
> > As part of this, students are asked to, in the MultiSeq window,
> > select Tools -> STAMP alignment options -> ok to perform a STAMP
> > alignment with the default settings. However, this freezes for my
> > students. At first I thought this was Windows only but it seems to
> > affect both Windows and Mac.
> >
> > Thanks for your help! I'm not sure where else would make sense to
> > report this issue.
> >
> > Regards,
> >
> > Phillip Compeau
>
> --
> 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/ 

-- 
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/