VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 02 2020 - 14:30:33 CST

Hi,
  There's been some ongoing trouble with the server that hosts
these DB files for multiseq. As of today, all of the database files
have been re-tested, and the only issue we continue to see is a
problem with the SCOP database, which they're still checking on.
I'm hoping this is resolved more permanently after the databases
are all migrated to a new web server. This has been complicated
for me to try and keep tabs on because all of the databases are
created, stored, and stored by a different research group.
Although they are at U. Illinois, it's the same level of complexity
ironing this out as if they were in Fiji. :-)

Best,
  John Stone

On Mon, Jul 13, 2020 at 04:34:50PM +0000, Julia Steckner wrote:
> Hello,
>
> I have been having trouble downloading databases for Multiseq. Upon
> opening, it asks me if I'd like to download some updates, which always
> fail. Then going into the "preferences" menu, I am given an option to
> download even more data, which also fails. It appears that the data
> sources have been moved. Is it possible to manually download them? When I
> attempt to do so, the files end up overwritten.
>
> Thank you very much,
>
> Julia
>
> (The error messages look like this:)
>
> vmd > MultiSeq Info) Retrieving multiseq db version from:
> http://www.scs.illinois.edu/multiseq/r3/versions_LINUXAMD64.txt
> http://www.scs.illinois.edu/multiseq/r3/versions_LINUXAMD64.txt is not
> available: HTTP/1.1 301 Moved Permanently
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.scs.illinois.edu/multiseq/r3/versions.txt
> http://www.scs.illinois.edu/multiseq/r3/versions.txt is not available:
> HTTP/1.1 301 Moved Permanently
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions_LINUXAMD64.txt
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions_LINUXAMD64.txt is
> not available: HTTP/1.1 404 Not Found
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions.txt
> Starting... Done!
> MultiSeq Info) Downloading
> http://www.scs.uiuc.edu/multiseq/r3/db/speclist.txt.gz to
> /home/julia/vmd-1.9.3/speclist.txt.gz
> http://www.scs.uiuc.edu/multiseq/r3/db/speclist.txt.gz is not available:
> HTTP/1.1 301 Moved Permanently
> MultiSeq Error)
> /home/julia/vmd-1.9.3/speclist.txt.gz is not available.
> while executing
> "::MultiSeqDialog::downloadMetadata $url $metadataDir [lindex [split $url
> /] end] $key $version"
> MultiSeq Info) Downloading
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/db/speclist.txt.gz to
> /home/julia/vmd-1.9.3/speclist.txt.gz
> Starting................................................. Done!
> MultiSeq Info) Unzipping speclist.txt.gz
> MultiSeq Info) Downloading
> http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.hie.scop.txt_1.69 to
> /home/julia/vmd-1.9.3/dir.hie.scop.txt_1.69
> http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.hie.scop.txt_1.69 is not
> available: HTTP/1.1 404 Not Found
> MultiSeq Error)
> /home/julia/vmd-1.9.3/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.uiuc.edu/multiseq/r3/db/dir.hie.scop.txt_1.69 to
> /home/julia/vmd-1.9.3/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) Downloading
> http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.69 to
> /home/julia/vmd-1.9.3/dir.des.scop.txt_1.69
> http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.69 is not
> available: HTTP/1.1 404 Not Found
> MultiSeq Error)
> /home/julia/vmd-1.9.3/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.uiuc.edu/multiseq/r3/db/dir.des.scop.txt_1.69 to
> /home/julia/vmd-1.9.3/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: /home/julia/.multiseqrc
> MultiSeq Info) Metadata directory: /home/julia/vmd-1.9.3
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.scs.illinois.edu/multiseq/r3/versions_LINUXAMD64.txt
> http://www.scs.illinois.edu/multiseq/r3/versions_LINUXAMD64.txt is not
> available: HTTP/1.1 301 Moved Permanently
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.scs.illinois.edu/multiseq/r3/versions.txt
> http://www.scs.illinois.edu/multiseq/r3/versions.txt is not available:
> HTTP/1.1 301 Moved Permanently
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions_LINUXAMD64.txt
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions_LINUXAMD64.txt is
> not available: HTTP/1.1 404 Not Found
> MultiSeq Error) message: Failed to retrieve version file.
> MultiSeq Info) Retrieving multiseq db version from:
> http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions.txt
> Starting... Done! 

-- 
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/