VMD-L Mailing List

From: Alexander Howard (alexhoward_at_nevada.unr.edu)
Date: Fri Jul 30 2021 - 19:03:22 CDT

Hello!
I'm currently working through the VMD tutorial and am struggling to
properly download the necessary databases for MultiSeq to function. Given a
cursory look at the errors I'm getting it seems that the .TXT file being
used to retrieve multiseq database versions (
http://faculty.scs.illinois.edu/schulten/multiseq/r3/versions.txt) is
referencing two broken links at the moment:
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.hie.scop.txt_1.69
and
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.des.scop.txt_1.69.
It looks like the urls are now
http://faculty.scs.illinois.edu/schulten/multiseq/r3/db/dir.hie.scop.txt_1.69
and
http://faculty.scs.illinois.edu/schulten/multiseq/r3/db/dir.des.scop.txt_1.69
but VMD isn't being redirected to those pages.

Sample error:
MultiSeq Info) Downloading
https://urldefense.com/v3/__http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.hie.scop.txt_1.69__;!!DZ3fjg!s3WMD22x2Z6F5R65Sy1KBG6Yxu-BpRdfILJ8g2pjD6ytF5KiyR7sjSerCPIlXdwE_Q$ to
C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.hie.scop.txt_1.69
https://urldefense.com/v3/__http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.hie.scop.txt_1.69__;!!DZ3fjg!s3WMD22x2Z6F5R65Sy1KBG6Yxu-BpRdfILJ8g2pjD6ytF5KiyR7sjSerCPIlXdwE_Q$ is not
available: HTTP/1.1 404 Not Found
MultiSeq Error)
C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.hie.scop.txt_1.69 is
not available.
    while executing
"::MultiSeqDialog::downloadMetadata $url $metadataDir [lindex [split $url
/] end] $key $version"
MultiSeq Info) Downloading
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.hie.scop.txt_1.69
to C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.hie.scop.txt_1.69
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.hie.scop.txt_1.69
is not available: HTTP/1.1 301 Moved Permanently
MultiSeq Info) Downloading
https://urldefense.com/v3/__http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.69__;!!DZ3fjg!s3WMD22x2Z6F5R65Sy1KBG6Yxu-BpRdfILJ8g2pjD6ytF5KiyR7sjSerCPIW9pINKQ$ to
C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.des.scop.txt_1.69
https://urldefense.com/v3/__http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.69__;!!DZ3fjg!s3WMD22x2Z6F5R65Sy1KBG6Yxu-BpRdfILJ8g2pjD6ytF5KiyR7sjSerCPIW9pINKQ$ is not
available: HTTP/1.1 404 Not Found
MultiSeq Error)
C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.des.scop.txt_1.69 is
not available.
    while executing
"::MultiSeqDialog::downloadMetadata $url $metadataDir [lindex [split $url
/] end] $key $version"
MultiSeq Info) Downloading
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.des.scop.txt_1.69
to C:/Alex/Lab_Files/Workshops/VMD/vmd-tutorial-files/dir.des.scop.txt_1.69
http://www.scs.illinois.edu/schulten/multiseq/r3/db/dir.des.scop.txt_1.69
is not available: HTTP/1.1 301 Moved Permanently

I've tried manually downloading these two files on my own and keeping them
in the same directory as the rest of the database files but that doesn't
seem to work as they get overwritten during the rest of the setup process.
Any suggestions? Without these files I'm currently unable to make the Stamp
Structural Alignment function work.
I'm aware that this was discussed last year but I hope this might help in
some way.
Thanks!
- Alex