VMD-L Mailing List

From: Greipel.Joachim_at_mh-hannover.de
Date: Wed Mar 02 2016 - 03:58:28 CST

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/

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