VMD-L Mailing List

From: Phillip Compeau (pcompeau_at_andrew.cmu.edu)
Date: Tue Nov 30 2021 - 10:27:03 CST

Yes, it was my post. I would be happy to report it elsewhere; it would
be a good thing to report in a VMD bug tracker, but I am unaware if this
exists.

I'm releasing an online course that uses Multiseq, and I would hate to
have to remove the part about stamp alignment because I think it's
useful for learners and good exposure for the software.

Happy to connect off this thread if there's someone on the VMD side who
can look into this.

Thanks!

Phillip

On 11/30/21 8:45 AM, 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 ;-)
>
> 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).
>
> 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).
>
> MultiSeq Info) Downloadinghttp://www.scs.uiuc.edu/multiseq/r3/db/dir.hie.scop.txt_1.69 to C:/Users/stefa/work/test/vmd/multiseq/dir.hie.scop.txt_1.69
> http://www.scs.uiuc.edu/multiseq/r3/db/dir.hie.scop.txt_1.69 is not available: HTTP/1.1 301 Moved Permanently
> MultiSeq Info) Downloadinghttp://www.scs.uiuc.edu/multiseq/r3/db/dir.des.scop.txt_1.69 to C:/Users/stefa/work/test/vmd/multiseq/dir.des.scop.txt_1.69
> http://www.scs.uiuc.edu/multiseq/r3/db/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.
>
> Just thought I'd confirm the earlier post -- any insights / hints would
> be appreciated.
>
> Best,
> Stefan
>