VMD-L Mailing List

From: Damian Loska (damian.loska_at_gmail.com)
Date: Sun Aug 30 2009 - 11:42:14 CDT

Hi
I have a problem with MultiSeq
I'm learning how to use VMD from tutorials.

When I following by this tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node6.html
error messages appears

When I open Extensions -> Analysis -> MultiSeq in terminal apperas
information about errors:

MultiSeq Info) MultiSeq r3b10
MultiSeq Reference) In any publication of scientific results based
completely or
MultiSeq Reference) in part on the use of MultiSeq, please reference:
MultiSeq Reference) Elijah Roberts, John Eargle, Dan Wright, and Zaida
Luthey-
MultiSeq Reference) Schulten. MultiSeq: Unifying sequence and structure data
for
MultiSeq Reference) evolutionary analysis. BMC Bioinformatics. 2006,7:382.
MultiSeq Info) Setting new temp options to /usr/tmp
multiseq-9034367100817322
MultiSeq Info) Loading multiseq resource file: /root/.multiseqrc
MultiSeq Info) Loaded multiseq preferences.
MultiSeq Info) Retrieving multiseq db version from:
http://www.scs.uiuc.edu/multiseq/r3/versions_LINUX.txt
MultiSeq Error) message: couldn't open
"/usr/tmp/multiseq-9034367100817322.versions.txt": no such file or directory
MultiSeq Info) Retrieving multiseq db version from:
http://www.scs.uiuc.edu/multiseq/r3/versions.txt
MultiSeq Error) message: couldn't open
"/usr/tmp/multiseq-9034367100817322.versions.txt": no such file or directory
MultiSeq Info) Retrieving multiseq db version from:
http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions_LINUX.txt
MultiSeq Error) message: couldn't open
"/usr/tmp/multiseq-9034367100817322.versions.txt": no such file or directory
MultiSeq Info) Retrieving multiseq db version from:
http://www.ks.uiuc.edu/Research/vmd/multiseq/r3/versions.txt
MultiSeq Error) message: couldn't open
"/usr/tmp/multiseq-9034367100817322.versions.txt": no such file or directory
MultiSeq Info) Retrieving multiseq db version from:
/usr/local/lib/vmd/plugins/noarch/tcl/multiseq2.1/versions_LINUX.txt
MultiSeq Info) Retrieving multiseq db version from:
/usr/local/lib/vmd/plugins/noarch/tcl/multiseq2.1/versions.txt
Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.

I checked this link:
http://www.scs.uiuc.edu/multiseq/r3/versions_LINUX.txt- there's no any
file.

Next, when I try Tools --> Stamp Structural Alignment --> OK
the error message appears:
The STAMP alignment failed with the following
error message:
couldn't open
"/usr/tmp/multiseq-7923878160269874.start.domain
":no such file or directory"

and information in terminal:
^T^TUnable to open file /usr/tmp/multiseq-9034367100817322.0.pdb for writing
ERROR) Unable to open file /usr/tmp/multiseq-9034367100817322.0.pdb of type
pdb for writing frames.
Unable to open file /usr/tmp/multiseq-9034367100817322.1.pdb for writing
ERROR) Unable to open file /usr/tmp/multiseq-9034367100817322.1.pdb of type
pdb for writing frames.
MultiSeq Error)
The selection in sequence 1j4n_X was not of the same type as the other
sequences and can not be aligned to them.
    while executing
"error "The selection in sequence [::SeqData::getName $sequenceID] was not
of the same type as the other sequences and can not be aligned to them.""
    (procedure "::STAMP::alignStructures" line 53)
    invoked from within
"::STAMP::alignStructures $regionSequenceIDs $scan $scanslide $scanscore
$slowscan $npass"

How could I solve this problem?
I use Linux Ubuntu 9.04, and VMD 1.8.7beta5,

Thanks