From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Thu Oct 12 2017 - 01:58:03 CDT

Hi John,

again, thank you for your offer of help.

Given my schedule, I won't have time to try anything for the next
few weeks. I believe you posted instructions a while back how to
recompile newer vmds (>= 1.9.3) against older cuda (Optix?? -- not
important!) libraries, and when I find time, I'll give this a try.

Alternatively, I may then ask for help about recompiling the webpdb
plugin for 1.9.2 -- I naively assumed this was a tcl script, where one just
needed to edit web addresses and the like ..

Thanks again, best regards,

Stefan Boresch

On Wed, Oct 11, 2017 at 02:43:24PM -0500, John Stone wrote:
> Hi Stefan,
> Okay, that's useful information. The GeForce 4xx and 5xx GPUs (Fermi generation hardware)
> are no longer supported by current versions of CUDA or OptiX, so the only way to make a new
> build of VMD that runs on them is to compile against old versions of CUDA. If you expect these
> machines to be taken out of service soon, then it may not be worth the trouble to compile a
> special VMD build for them, but if you think they'll be used for another year or more, then
> it might be useful to have a new VMD build for them. While I have already set the VMD 1.9.4
> build scripts to use the current versions of CUDA, etc, you could in principle still compile
> it for older toolkit versions. If you're interested in doing this, let me know. If you think
> these machines will go away soon, then I wouldn't worry about it much. If you wanted to
> recompile just the VMD webpdb plugin, that would let the most common web-based PDB download
> work for you. I can tell you how to do that (or do it for you) and it's much less of a
> time/effort investment than recompiling all of VMD and its associated dependencies.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Oct 11, 2017 at 09:01:56PM +0200, Stefan Boresch wrote:
> > 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
> > > > ¬ ([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.
> > > > -----------------------------------------------------------------------------------------¬
> > > > puts -nonewline "Enter PDB code: "¬
> > > > flush stdout¬
> > > > set name [gets stdin]¬
> > > > puts "Getting $name"¬
> > > > package require http¬
> > > > set handle [::http::geturl¬ [2]http://files.rcsb.org/view/$name.pdb
> > > > set pdb_file [open $name.pdb a]¬
> > > > puts $pdb_file [::http::data $handle]¬
> > > > mol load pdb $name.pdb¬
> > > > -----------------------------------------------------------------------------------------¬
> > > >
> > > > * you will have to save it into the working directory of vmd¬
> > > > * start vmd¬
> > > > * in the tkconsole or the shell at the VMD prompt type¬
> > > > * source name_of_the_script_file¬
> > > > * it will ask for a PDB code -- only enter the 4 letter ID¬
> > > > * it will do some webpage parsing - download the file to your working
> > > > directory and also as the last line of the code read load it into
> > > > VMD as well.¬
> > > > * At the time I wrote this, I did not test it. Neither is it tested
> > > > now so use cautiously. ¬
> > > >
> > > > On Wed, Oct 11, 2017 at 7:40 PM, Stefan Boresch
> > > > <[3]stefan_at_mdy.univie.ac.at> wrote:
> > > >
> > > > Hi everyone,
> > > >
> > > > I understand that some months ago the PDB changed its website layout,
> > > > breaking the automated dowload of pdb structures into vmd. I know that
> > > > this is fixed in the 1.9.4 series.
> > > >
> > > > However, I have several older machines, mostly running 1.9.2, at most
> > > > 1.9.3,
> > > > which hardware wise (old nvidia gpus etc) either don't play nice with
> > > > 1.9.4
> > > > or where updating is 'painful'. Is this (out of vmd's control) broken
> > > > pdb load functionality in some TCL script, which I could update; in
> > > > other
> > > > words, is there a (relatively) easy way to restore the functionality in
> > > > vmd versions prior to 1.9.4?
> > > >
> > > > Thanks,
> > > >
> > > > Stefan (Boresch)
> > > >
> > > > --
> > > > Best,
> > > > /A
> > > >
> > > > References
> > > >
> > > > Visible links
> > > > 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html
> > > > 2. http://files.rcsb.org/view/$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/
>
> --
> 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/
>