VMD-L Mailing List

From: l.spitzer_at_fr.fournierpharma.com
Date: Tue Aug 29 2006 - 11:18:08 CDT

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
>>
>>
>>
>
>
>
>
>