VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 29 2006 - 12:55:03 CDT

Hi,
  Proxies are configured via the Tcl http package. You should be able
to configure your proxy in your VMD .vmdrc file with commands similar
to these:
  package require http
  ::http::config -proxyhost proxy.ks.uiuc.edu
  ::http::config -proxyport 80

The http package manual page is here:
  http://www.tcl.tk/man/tcl8.4/TclCmd/http.htm

I think that by doing the steps above, the problem with his multiseq
connections will go away. Please try that and let us know how it goes.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 29, 2006 at 12:20:04PM -0500, Elijah Roberts wrote:
> Ah, ok. So if you wait then eventually the MultiSeq dialog appears and
> you can continue working, but it takes a long time to timeout every time
> you try to open it. I don't know of any way to have VMD use a proxy
> server and there is no flag to bypass the version check. I will add such
> a flag to the list of fixes for the next release. In the mean time if
> you want to skip the automatic version checking, you will have to make a
> little change to the tcl file that does the updates. In the file:
>
> C:/Program Files/University of
> Illinois/VMD/plugins/noarch/tcl/multiseqdialog1.0/multiseqdialog.tcl
>
>
> change line 757 from this:
>
> foreach location [list $platformInfoURL $infoURL $backupPlatformInfoURL
> $backupInfoURL $platformInfoFile $infoFile] {
>
>
> to this:
>
> foreach location [list $platformInfoFile $infoFile] {
>
>
> That should cause the online version checking to be skipped.
>
> Elijah
>
>
> l.spitzer_at_fr.fournierpharma.com wrote:
> >
> >
> >Here is the whole message in the console :
> >
> > Info) VMD for WIN32, version 1.8.5 (August 25, 2006)
> >Info) http://www.ks.uiuc.edu/Research/vmd/
> >Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >Info) Please include this reference in published work using VMD:
> >Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >Info) -------------------------------------------------------------
> >Info) OpenGL renderer: Intel 915G
> >Info) Features: STENCIL MDE CVA MTX PP
> >Info) GLSL rendering mode is NOT available.
> >Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> >Info) Spaceball driver not installed. Spaceball interface disabled.
> >Info) No joysticks found. Joystick interface disabled.
> >Found 57 plugins or data handlers in directory
> > 'C:/Program Files/University of
> >Illinois/VMD/plugins/WIN32/molfile'.
> >vmd > Info) Using plugin pdb for structure file C:/Documents and
> >Settings/spitzl
> >/Mes documents/ERRalpha/full pdb/2ewp_A.pdb
> >Info) Using plugin pdb for coordinates from file C:/Documents and
> >Settings/spitz
> >l/Mes documents/ERRalpha/full pdb/2ewp_A.pdb
> >Info) Determining bond structure from distance search ...
> >Info) Analyzing structure ...
> >Info) Atoms: 1776
> >Info) Bonds: 1808
> >Info) Residues: 224
> >Info) Waters: 0
> >Info) Segments: 1
> >Info) Fragments: 1 Protein: 1 Nucleic: 0
> >Info) Finished with coordinate file C:/Documents and Settings/spitzl/Mes
> >documen
> >ts/ERRalpha/full pdb/2ewp_A.pdb.
> >Info) Using plugin pdb for structure file C:/Documents and
> >Settings/spitzl/Mes d
> >ocuments/ERRalpha/full pdb/1xb7.pdb
> >Info) Using plugin pdb for coordinates from file C:/Documents and
> >Settings/spitz
> >l/Mes documents/ERRalpha/full pdb/1xb7.pdb
> >Info) Determining bond structure from distance search ...
> >Info) Analyzing structure ...
> >Info) Atoms: 1826
> >Info) Bonds: 1763
> >Info) Residues: 309
> >Info) Waters: 84
> >Info) Segments: 1
> >Info) Fragments: 89 Protein: 4 Nucleic: 0
> >Info) Finished with coordinate file C:/Documents and Settings/spitzl/Mes
> >documen
> >ts/ERRalpha/full pdb/1xb7.pdb.
> >MultiSeq Info) MultiSeq v2.0
> >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 c: multiseq-817239950326
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.scs.uiuc.
> >edu/multiseq/versions_WIN32.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.scs.uiuc.
> >edu/multiseq/versions.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.ks.uiuc.e
> >du/Research/vmd/multiseq/versions_WIN32.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.ks.uiuc.e
> >du/Research/vmd/multiseq/versions.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from: C:/Program
> >Files/Uni
> >versity of Illinois/VMD/plugins/noarch/tcl/multiseq2.0/versions_WIN32.txt
> >MultiSeq Info) Metadata directory: C:/Documents and Settings/spitzl
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.scs.uiuc.
> >edu/multiseq/versions_WIN32.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.scs.uiuc.
> >edu/multiseq/versions.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.ks.uiuc.e
> >du/Research/vmd/multiseq/versions_WIN32.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from:
> >http://www.ks.uiuc.e
> >du/Research/vmd/multiseq/versions.txt
> >MultiSeq Error) message: couldn't open socket: connection timed out
> >MultiSeq Info) Trying to retrieve multiseq db version from: C:/Program
> >Files/Uni
> >versity of Illinois/VMD/plugins/noarch/tcl/multiseq2.0/versions_WIN32.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.
> >
> >To answer your question, the different messages appear after some minutes
> >(I didn't measur exactly, but it took quite 2 minutes for all this message
> >to appear, until I can use VMD again!)
> >Thus, when I launch it, the preference window appears automatically once
> >all of this is done!
> >
> >Hope this will help you,
> >
> >Thanks in advance,
> >
> >--------------------
> >Luc SPITZER
> >Computer Assisted Drug Design (IT)
> >Laboratoires Fournier (Member of Solvay Group)
> >50, rue de Dijon
> >F-21121 DAIX
> >+333.80.44.75.00
> >l.spitzer_at_fr.fournierpharma.com
> >
> >
> >
> >
> > Elijah Roberts
> > <erobert3_at_scs.uiu Pour :
> > l.spitzer_at_fr.fournierpharma.com
> > c.edu> cc :
> > owner-vmd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu
> > Envoyé par : Objet : vmd-l: Re: Réf. :
> > Re: vmd-l: vmd-l : VMD1.8.5 : multiseq db
> > owner-vmd-l_at_ks.ui
> > uc.edu
> >
> >
> > 29/08/2006 17:45
> >
> >
> >
> >
> >
> >
> >That's interesting. Can you send me the entire console text after you
> >have tried to open MultiSeq? Also, how long does it take for the
> >
> >couldn't open socket: connection timed out
> >
> >message to appear and do you see one or several of them?
> >
> >Elijah
> >
> >l.spitzer_at_fr.fournierpharma.com wrote:
> >
> >>Dear Elijah,
> >>
> >>Thank you very much for your answer...
> >>But I must have missed one step, because when I launch multiseq, I am
> >>
> >never
> >
> >>asked if I want to download the updates...it starts automatically!
> >>I am just asked to choose the directory in which I want to save metadata.
> >>
> >>(For information, I run VMD on windows system...)
> >>
> >>So is there a way I can either parametirize the connection to your site
> >>
> >via
> >
> >>the proxy?or to not download automatically the updates?
> >>
> >>Thanks in adavance,
> >>
> >>--------------------
> >>Luc SPITZER
> >>Computer Assisted Drug Design (IT)
> >>Laboratoires Fournier (Member of Solvay Group)
> >>50, rue de Dijon
> >>F-21121 DAIX
> >>+333.80.44.75.00
> >>l.spitzer_at_fr.fournierpharma.com
> >>
> >>
> >>
> >>
> >
> >
> >> Elijah Roberts
> >>
> >
> >
> >> <erobert3_at_scs.uiu Pour :
> >>
> >l.spitzer_at_fr.fournierpharma.com
> >
> >> c.edu> cc :
> >>
> >vmd-l_at_ks.uiuc.edu
> >
> >> Envoyé par : Objet : Re: vmd-l: vmd-l
> >>
> >: VMD1.8.5 : multiseq db
> >
> >> owner-vmd-l_at_ks.ui
> >>
> >
> >
> >> uc.edu
> >>
> >
> >
> >
> >
> >
> >
> >> 29/08/2006 16:08
> >>
> >
> >
> >
> >
> >
> >
> >>
> >>
> >>Yes, when the dialog appears asking if you want to download the updates
> >>now, just click "No". You can also download them manually if you find
> >>that you need the data they contain: taxonomy and enzyme information
> >>about sequences and structures.
> >>
> >>Elijah
> >>
> >>
> >>l.spitzer_at_fr.fournierpharma.com wrote:
> >>
> >>
> >>>Dear All,
> >>>
> >>>I just installed the new version of VMD on my system (1.8.5) and tried
> >>>
> >to
> >
> >>>use the multiseq alignment tool.
> >>>
> >>>But to my surprise, it tried to connect to a distant server :
> >>>MultiSeq Info) Trying to retrieve multiseq db version from:
> >>>http://www.scs.uiuc.edu/multiseq/versions.txt
> >>>
> >>>Due to proxy limitations, I cannot download those requested files :
> >>>MultiSeq Error) message: couldn't open socket: connection timed out
> >>>
> >>>Is there a way I can skip this step when launching multiseq, or use this
> >>>files located in a local directory on my system?
> >>>
> >>>Thank in advance for your answer,
> >>>
> >>>--------------------
> >>>Luc SPITZER
> >>>Computer Assisted Drug Design (IT)
> >>>Laboratoires Fournier (Member of Solvay Group)
> >>>50, rue de Dijon
> >>>F-21121 DAIX
> >>>+333.80.44.75.00
> >>>l.spitzer_at_fr.fournierpharma.com
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >>
> >
> >
> >
> >
> > 

-- 
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