VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Oct 11 2017 - 03:18:41 CDT

I posted a fix for earlier builds a couple months back. Here (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html) it is
again.

Save the following code in a script file.

-----------------------------------------------------------------------------------------
puts -nonewline "Enter PDB code: "
flush stdout
set name [gets stdin]
puts "Getting $name"
package require http
set handle [::http::geturl http://files.rcsb.org/view/$name.pdb]
set pdb_file [open $name.pdb a]
puts $pdb_file [::http::data $handle]
mol load pdb $name.pdb
-----------------------------------------------------------------------------------------

> - you will have to save it into the working directory of vmd
> - start vmd
> - in the tkconsole or the shell at the VMD prompt type
> - source name_of_the_script_file
> - it will ask for a PDB code -- only enter the 4 letter ID
> - it will do some webpage parsing - download the file to your working
> directory and also as the last line of the code read load it into VMD as
> well.
> - At the time I wrote this, I did not test it. Neither is it tested
> now so use cautiously.
>
>
On Wed, Oct 11, 2017 at 7:40 PM, Stefan Boresch <stefan_at_mdy.univie.ac.at>
wrote:

> Hi everyone,
>
> I understand that some months ago the PDB changed its website layout,
> breaking the automated dowload of pdb structures into vmd. I know that
> this is fixed in the 1.9.4 series.
>
> However, I have several older machines, mostly running 1.9.2, at most
> 1.9.3,
> which hardware wise (old nvidia gpus etc) either don't play nice with 1.9.4
> or where updating is 'painful'. Is this (out of vmd's control) broken
> pdb load functionality in some TCL script, which I could update; in other
> words, is there a (relatively) easy way to restore the functionality in
> vmd versions prior to 1.9.4?
>
> Thanks,
>
> Stefan (Boresch)
>
> 

-- 
Best,
/A