VMD-L Mailing List

From: Elijah Roberts (erobert3_at_scs.uiuc.edu)
Date: Tue Aug 29 2006 - 12:20:04 CDT

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
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>
>
>