VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Wed Oct 11 2017 - 03:52:04 CDT

Thank you -- Stefan

On Wed, Oct 11, 2017 at 09:18:41PM +1300, Ashar Malik wrote:
> 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