VMD-L Mailing List

From: Greipel.Joachim_at_mh-hannover.de
Date: Thu Mar 03 2016 - 01:12:02 CST

Hi,

yes, I'm interested in trying this! I would appreciate a modified version of
the source code.

Regards,
Joachim Greipel

greipel.joachim_at_mh-hannover.de

-----Ursprüngliche Nachricht-----
Von: John Stone [mailto:johns_at_ks.uiuc.edu]
Gesendet: Mittwoch, 2. März 2016 16:33
An: Greipel, Joachim Dr.
Cc: vmd-l_at_ks.uiuc.edu
Betreff: Re: WG: vmd-l: vmd and proxy settings

Hi,
  The 'webpdb' plugin creates a new Tcl interpreter instance, which has the
effect that it does not inherit or alter any state within the main VMD Tcl
interpreter. You could recompile the webpdb plugin to force it to use a
proxy if necessary, it would be a matter of modifying the source code to run
an extra Tcl_Eval() call to perfom the proxy setup akin to what you ran in
the main VMD Tcl interpreter.
If you're interested in trying this, I could probably make a modified
version that does this for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 02, 2016 at 09:58:28AM +0000, Greipel.Joachim_at_mh-hannover.de
wrote:
> Hi,
>
> I found a difference between "Download to local PDB file" and "Load
> into new molecule in VMD".
>
> 1. uses "vmdhttpcopy" to download PDB Files. -> is influenced by the
> proxy-settings in .vmdrc, works.
> 2. uses "mol new ..." to download PDB Files. This is supposedly
> located in ../plugins/LINUXAMD64/molfile/webpdbplugin.so and is NOT
> influenced by the proxy-settings. Doesn't work.
>
> Regards,
> Joachim
> --
> Dr. rer. nat. Joachim Greipel
>
> Med. Hochschule Hannover
> Biophysikalische Chemie OE 4350
> Carl-Neuberg-Str. 1
> 30625 Hannover
> Germany
> Fon: +49-511-532-3718
> Fax: +49-511-532-16-3718
> E-Mail: greipel.joachim_at_mh-hannover.de
>
>
> -----Ursprüngliche Nachricht-----
> Von: Greipel, Joachim Dr.
> Gesendet: Mittwoch, 2. März 2016 08:22
> An: 'John Stone'
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: AW: vmd-l: vmd and proxy settings
>
> Hi,
> Thank you, this works great for e.g.
>
> "Download to local PDB file"
>
> but as it seems not for
>
> "Load into new molecule in VMD".
>
> Response: "Error loading PDB: couldn't open socket: connection timed out"
>
> Hmm. What's the difference?
>
> Best Regards,
> Joachim Greipel
>
> --
> Dr. rer. nat. Joachim Greipel
>
> Med. Hochschule Hannover
> Biophysikalische Chemie OE 4350
> Carl-Neuberg-Str. 1
> 30625 Hannover
> Germany
> Fon: +49-511-532-3718
> Fax: +49-511-532-16-3718
> E-Mail: greipel.joachim_at_mh-hannover.de
>
>
> -----Ursprüngliche Nachricht-----
> Von: John Stone [mailto:johns_at_ks.uiuc.edu]
> Gesendet: Dienstag, 1. März 2016 17:22
> An: Greipel, Joachim Dr.
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: vmd and proxy settings
>
> 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 yourproxy.yourdomain.com
> ::http::config -proxyport 80
>
> Read more about using "::http::config" for proxies here:
> http://www.tcl.tk/man/tcl8.5/TclCmd/http.htm#M6
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Mar 01, 2016 at 11:59:03AM +0000,
> Greipel.Joachim_at_mh-hannover.de
> wrote:
> > Hi,
> >
> >
> >
> > we have VMD 1.9.2 installed on a couple of Linux workstations
> > (SLES
> 11.3,
> > CentOS 7.1). Loading PDB structures from the Web does not work,
> presumably
> > because of our http proxy. Where do I configure a proxy in VMD?
> >
> >
> >
> > Error Message when trying to load, e.g. 4PTI:
> >
> >
> >
> > "Error loading PDB: couldn't open socket: connection timed out
> >
> > ERROR) Could not read file 4PTI"
> >
> >
> >
> > Regards,
> >
> > Joachim
> >
> >
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics Beckman
> Institute for Advanced Science and Technology University of Illinois,
> 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

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

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