VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 11 2017 - 09:46:50 CDT

Hi,
  The script below is helful, but it only addresses the 'webpdb' part of the VMD updates we had
to make for the RCSB web site changes. To correct the behavior of VMD 1.9.4, updates were made
to a few places in VMD's webpdbplugin, qwikmd, and autopsf, pdbtool, etc.

Stefan, how old are the GPUs you said have trouble with VMD 1.9.4? What generation are they?
You can query them by running 'nvidia-smi' and it will report both the hardware and the
driver version number. If you can tell me what you've got I could estimate how difficult it
would be to either build a VMD 1.9.4 for your hardware, or to get your machines in sync with
current drivers so they can run VMD 1.9.4.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

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
> Â ([1]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html)
> it is again.
> Save the following code in a script file.
> -----------------------------------------------------------------------------------------Â
> puts -nonewline "Enter PDB code: "Â
> flush stdoutÂ
> set name [gets stdin]Â
> puts "Getting $name"Â
> package require httpÂ
> set handle [::http::geturl [2]http://files.rcsb.org/view/$name.pdb]Â
> set pdb_file [open $name.pdb a]Â
> puts $pdb_file [::http::data $handle]Â
> mol load pdb $name.pdbÂ
> -----------------------------------------------------------------------------------------Â
>
> * you will have to save it into the working directory of vmdÂ
> * start vmdÂ
> * in the tkconsole or the shell at the VMD prompt typeÂ
> * source name_of_the_script_fileÂ
> * it will ask for a PDB code -- only enter the 4 letter IDÂ
> * it will do some webpage parsing - download the file to your working
> directory and also as the last line of the code read load it into
> VMD as well.Â
> * At the time I wrote this, I did not test it. Neither is it tested
> now so use cautiously. Â
>
> On Wed, Oct 11, 2017 at 7:40 PM, Stefan Boresch
> <[3]stefan_at_mdy.univie.ac.at> wrote:
>
> Hi everyone,
>
> I understand that some months ago the PDB changed its website layout,
> breaking the automated dowload of pdb structures into vmd. I know that
> this is fixed in the 1.9.4 series.
>
> However, I have several older machines, mostly running 1.9.2, at most
> 1.9.3,
> which hardware wise (old nvidia gpus etc) either don't play nice with
> 1.9.4
> or where updating is 'painful'. Is this (out of vmd's control) broken
> pdb load functionality in some TCL script, which I could update; in
> other
> words, is there a (relatively) easy way to restore the functionality in
> vmd versions prior to 1.9.4?
>
> Thanks,
>
> Stefan (Boresch)
>
> --
> Best,
> /A
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html
> 2. http://files.rcsb.org/view/$name.pdb
> 3. mailto:stefan_at_mdy.univie.ac.at 

-- 
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/