VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 15 2011 - 15:51:38 CDT

Tiago,
  I'm guessing that for some reason, your http::config settings are
not affecting the webpdb download the way I had expected. I'll have
to investigate the reason for this and get back to you. I don't think
that the problem has to do with too short of a timeout, most likely
it's just not using the proxy as we had hoped it would. If I come up
with a solution for this, I'll let you know. In the short term, you
can use a short script to download the structures yourself until the
webpdb plugin has been made to cooperate. I may have to create a modified
version of the webpdb plugin for you in order to get around this problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 14, 2011 at 07:25:02AM -0700, tiago sobreira wrote:
> Hi John
> The http::config fix part of the problem. Now I can download a PDB with
> the command like that:
> puts [http::data [http::geturl
> http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1fmo]]
> But I still can not load a molecule directly with mol new
> vmd > mol new 1fmo
> Error loading PDB: couldn't open socket: connection timed out
> ERROR) Could not read file 1fmo
> Unable to load file '1fmo' using file type 'webpdb'.
> Is it possible to increase timeout ?
> Thanks
> Tiago
>
> ----------------------------------------------------------------------
>
> De: John Stone <johns_at_ks.uiuc.edu>
> Para: tiago sobreira <tiagosobreira_at_yahoo.com.br>
> Cc: vmd-l_at_ks.uiuc.edu
> Enviadas: Terc,a-feira, 12 de Abril de 2011 16:09:33
> Assunto: Re: vmd-l: webpdb load problem
>
> Hi,
> Try adding Tcl ::http::config calls to your .vmdrc file, to setup
> your local web proxy:
> http://www.tcl.tk/man/tcl8.5/TclCmd/http.htm
> http://www.tcl.tk/man/tcl8.5/TclCmd/http.htm#M6
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 12, 2011 at 11:48:29AM -0700, tiago sobreira wrote:
> > Hi
> > I am trying to load a molecule direct from internet and I get the
> > following error menssagem:
> > vmd > mol new 1bxs
> > Error loading PDB: couldn't open socket: connection timed out
> > ERROR) Could not read file 1bxs
> > Unable to load file '1bxs' using file type 'webpdb'.
> > I am inside of network with proxy. Is it necessary open some door?
> > Thanks for the attention,
> > Tiago Jose Paschoal Sobreira
> > Pesquisador em Biologia Computacional
> > Laboratorio Nacional de Biociencias (LNBio)
>
> --
> 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 

-- 
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