VMD-L Mailing List

From: Julia Steckner (julia.steckner_at_uwaterloo.ca)
Date: Mon Jul 13 2020 - 11:34:50 CDT

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!