From: John Stone (
Date: Wed Dec 01 2021 - 00:49:28 CST


On Tue, Nov 30, 2021 at 02:45:40PM +0100, Stefan Boresch wrote:
> Hi,
> there was a mail to the list a few days ago, to which I can't answer
> anymore since I too quickly deleted it, but I just want to confirm the
> issue (and it's also biting me in a course I am teaching ;-)

The other note described hanging behavior, so that's a little different from
what you're describing below.

> On Windows 1.9.4a53 the multiseq tool does not really work; even for the
> very simple example from the tutorial. (The tutorial example works fine
> with 1.9.3).

Do your windows systems have the TEMPDIR environment variable set?
If so, what is it set to?

This can impact the behavior of VMD's use of temporary files generally,
and that may also affect multiseq's use of STAMP, although since we didn't
develop multiseq I would need to look at the code to determine what exactly
it is trying to do there..

> The STAMP alignment exercise with 1.9.4a53 (Windows) fails, because
> temporary files want apparently be written to C:\ which obviously
> doesn't work. The console output on 1.9.3 shows the same location, but
> there things work, so I assume it's writing these files to some
> legitimate location. (I failed to locate them ..).
> Additional observations:
> 1) On all platforms, the multiseq tool tries to download two files (or
> the same file from two locations) which are/is not available anymore
> (but at least for the tutorial example this seems irrelevant).

I'm aware of the download problems, we had reported this to the team
that has developed multiseq, but they haven't managed to resolve the
problem with their web server. I will send them a note reminding them
to dig into this again.

> MultiSeq Info) Downloading to C:/Users/stefa/work/test/vmd/multiseq/dir.hie.scop.txt_1.69
> is not available: HTTP/1.1 301 Moved Permanently
> MultiSeq Info) Downloading to C:/Users/stefa/work/test/vmd/multiseq/dir.des.scop.txt_1.69
> is not available: HTTP/1.1 301 Moved Permanently
> MultiSeq Info) Saving multiseq resource file: C:/Users/stefa/multiseq.rc
> 2) Running Linux 1.9.4a55 under WSL/Windows 11 (with WSLg) mostly
> works (fonts too small, but that's a generic WSLg issue). The
> multiseq exercise, however, also fails because the menus of the
> multiseq tool become unresponsive. All primary menus (molecule,
> graphics, display ..) work just fine.

That's an interesting issue. I assume that if you run natively
on Linux this hanging behavior for multiseq doesn't occur?

> Just thought I'd confirm the earlier post -- any insights / hints would
> be appreciated.

The linux version uses a different version of Tcl/Tk than the
Windows/Mac versions, which hasn't previously shown any hanging
behavior w/ Multiseq, but it's possible that WSLg triggers some
different behavior with Tk GUI processing that leads to a hang
for a different reason than the Windows/Mac-native builds.
As with the other email, a big question is whether or not you
see any error messages logged in the main VMD text console or not.

  John Stone

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349