VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 31 2009 - 14:37:44 CDT

Hi,
  Since the final version of VMD 1.8.7 is release, please do upgrade.
We can't really offer continuing support for beta versions once the final
versions are available.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 31, 2009 at 02:25:30PM -0500, Kirby Vandivort wrote:
> Damian,
>
> It looks like the directory /usr/tmp/ either doesn't exist on your system,
> or the user you are running vmd as doesn't have permission to write to that
> directory.
>
> There are a couple of different issues that you have listed. The first one
> is where MultiSeq tries to download updated database information. The
> errors with the LINUX files are normal; we don't have (at this time)
> specific versions of the database information files for LINUX. In my mind,
> I'm thinking of a way that we can rewrite that code to be more clear for
> the users, but, for now, it is what it is. So, you don't have to worry
> about the LINUX part. BUT, regardless, you shouldn't be seeing errors
> opening files in /usr/tmp/, which is leading me to think that /usr/tmp/ on
> your system is nonexistent or has inadequate permissions.
>
> If you can check that, that will give me more information on how to proceed
> with your situation. Also, VMD 1.8.7 final has been released. While there
> weren't a lot of changes between beta 5 and the final, you might consider
> grabbing the latest and greatest.
>
> Thanks,
>
> Kirby
>
>
>
> Damian Loska wrote:
> >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
> >
>
>
> --
>
> Kirby Vandivort Theoretical and
> Senior Research Programmer Computational Biophysics
> Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
> http://www.ks.uiuc.edu/~kvandivo/ University of Illinois
> Phone: (217) 244-1928 405 N. Mathews Ave
> Fax : (217) 244-6078 Urbana, IL 61801, USA 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078