VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Thu Sep 17 2009 - 11:54:44 CDT

Jeremias Corradi wrote:
> hi Kirby,
> thank you for your soon answer, you're right, i'm ussing VMD 1.8.7, and
> i see thousands of 'dots' appearing fairly fast at the beginning of the
> download process, but after some minutes, the process start to become
> slower until it seams to be unchangeable. I don't know if its possible
> to have some problems with the internet conection because i'm using a
> proxy conection in my workplace. I don't think that this is the problem
> because files "nodes.dmp" and "names.dmp" have been downloaded properly.
> The computer was downloading the gi_taxid_prot file all night long and
> it couldn't finish... i don't know how much time it would require...
>
> Thank you very much
> i just have to wait...!!!
>
> Jere
>

Jere,

Sounds like that is the problem. If the other files are downloading properly,
it sounds like this is just a size issue. Maybe your workplace has maximum
sizes for file transfers or something.

If you are continually unsuccessful, you could attempt to download the file
manually, though this takes several steps and could be easy to mess up.. The
URL is given in the console. You could download the .gz file to the directory
that it states, and then uncompress the gz file (it will uncompress into a file
that is 345,176,247 bytes). Then you would need to edit the .multisecrc file in
your home directory to have the following:

  <gi_tax_map>
   <version>
    20080726
   </version>

   <filename>
    gi_taxid_prot.dmp.gz
   </filename>
</gi_tax_map>

in it. We don't recommend the manual method because it could cause you to miss
out on updates and it is easy to make a mistake in the process.

Kirby

>
>
>
> ----- Original Message ----- From: "Kirby Vandivort" <kvandivo_at_ks.uiuc.edu>
> To: "Jeremias Corradi" <jcorradi_at_criba.edu.ar>
> Cc: "VMD-List" <vmd-l_at_ks.uiuc.edu>
> Sent: Thursday, September 17, 2009 12:44 PM
> Subject: Re: vmd-l: Installing Multiseq updates
>
>
>> Jeremias,
>>
>> I have checked our servers, and everything is working properly on our
>> end.
>>
>> The download for the gi_taxid_prot file (which is quite large) should
>> look
>> something like the following in your VMD console:
>>
>> MultiSeq Info) Downloading
>> http://www.scs.uiuc.edu/multiseq/r3/db/gi_taxid_prot.dmp.gz to
>> /folder/you've/listed/gi_taxid_prot.dmp.gz
>> Starting.......[thousands of dots deleted]...........................
>> Done!
>> MultiSeq Info) Unzipping gi_taxid_prot.dmp.gz
>>
>> The gi_taxid_prot.dmp.gz file that is downloaded is 55,866,735 bytes,
>> so it will
>> likely take a while, particularly if you have a slow internet
>> connection to the
>> US.
>>
>> Assuming you are using VMD 1.8.7, during the download VMD prints out a
>> 'dot'
>> each time it downloads 8 kilobytes. Are you seeing progress as the
>> download
>> continues?
>>
>> Kirby
>>
>> Jeremias Corradi wrote:
>>> Hi everyone, i'm new using vmd and i'm fascinated with all the tools
>>> that this program has to enrich my work., but I've found some little
>>> problems when I tried to run Multiseq, the program asks me for download
>>> some updates and spend hours triend to download the file called
>>> "gi_taxid_prot.dmp". I don't know if that is normal or if there is some
>>> problem with my installation, computer, windows vista, internet
>>> conection, or something else... If somebody can give me some advise I'll
>>> be very grateful
>>> thanks in advance
>>> Jere
>>>
>>> Jeremías Corradi
>>> INIBIBB
>>> Camino La Carrindanga Km7. CC857. B8000FWB.
>>> 54-291-4861201 (int. 124)
>>>
>>> Bahía Blanca, Argentina
>>
>>
>> --
>>
>> Kirby Vandivort Theoretical and
>> Senior Research Programmer Computational Biophysics
>> Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
>> http://www.ks.uiuc.edu/~kvandivo/ University of Illinois
>> Phone: (217) 244-1928 405 N. Mathews Ave
>> Fax : (217) 244-6078 Urbana, IL 61801, USA
>
>
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>
>
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>
> Jeremías Corradi
> INIBIBB
> Camino La Carrindanga Km7. CC857. B8000FWB.
> 54-291-4861201 (int. 124)
>
> Bahía Blanca, Argentina 

-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA