VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Wed Oct 11 2017 - 14:01:56 CDT

John,

thank you for the detailed reply (as always) and offer of help.

We have several old student machines
with GTX 4xx and GTX 5xx cards. vmd-1.9.3 runs, but occasionally
crashes (e.g. for quick surface -- this was, I believe, discussed on
this list a while ago).

Now, these machines really are for introductory course work only, used, e.g., to
visualize structures before/after manipulating them in some manner
outside vmd (we are a CHARMM/charmm-gui 'shop'). Thus, while I install
1.9.3 (or now 1.9.4) on new machines or on my desktop, I saw no
reason so far to upgrade these ancient course machines.

In any case, don't loose time over this; chances are good that these
machines will die of 'old age' sooner than later ..

I was really curious whether the 'webpdb part' of 1.9.2 could be 'patched'
to work again ..

Best regards,

Stefan (Boresch)

On Wed, Oct 11, 2017 at 09:46:50AM -0500, John Stone wrote:
> 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/