VMD-L Mailing List

From: Christopher McLean (C.J.McLean_at_leeds.ac.uk)
Date: Thu Feb 11 2010 - 03:18:29 CST

Thanks very much for this John,

I have installed it and the user has reported it working perfectly!

Thanks again

Chris

+------------------------------------------------+
| Chris McLean -- MaPS Linux systems manager |
| |
| Email: c.j.mclean_at_leeds.ac.uk |
| Support: http://www.maps.leeds.ac.uk/itsupport |
| WWW: http://mapsitdoc.leeds.ac.uk/ |
+------------------------------------------------+

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of John Stone
> Sent: 09 February 2010 16:08
> To: Axel Kohlmeyer; Christopher McLean; 'vmd-l_at_ks.uiuc.edu'
> Subject: Re: vmd-l: Blank thumbnails and non-working snapshots
>
> Hi,
> Ok, the bug appears to have only been in the viewmaster plugin itself
> and not VMD.
>
> Viewmaster was incorrectly saving/restoring material properties as a
> result of the new material properties that were added in VMD 1.8.7.
>
> I've attached a fixed version of the plugin script to this email.
> To use it, just gunzip it and then put the viewmaster.tcl file into
> your VMD installation directory, e.g.:
> /usr/local/lib/vmd/plugins/noarch/tcl/viewmaster2.2/
>
> Let me know if you still have any trouble after updating to the new
> viewmaster plugin.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 09, 2010 at 09:29:32AM -0600, John Stone wrote:
> >
> > Hi guys,
> > So, I just tested Axel's structure with a few pre-release versions
> > of VMD 1.8.7 as well as the older VMD 1.8.6 and 1.8.5 versions, and
> on
> > my Linux machine, the problem occurs on all of them, even VMD 1.8.6
> and 1.8.5.
> >
> > Interestingly, I find that if I create a fresh Viewmaster saved
> > session using VMD 1.8.4, it will load and display correctly in all of
> > the versions I've tested: VMD 1.8.4, 1.8.5, 1.8.6, and 1.8.7.....
> > I presume this may also be the case for viewmaster sessions created
> > with later versions up to some point.
> >
> > So, there's something about the contents of the saved session from
> the
> > new 1.8.7 version that's poisoning all these versions when loaded.
> > I'll have to figure out what it is and get back to you.
> >
> > In my testing so far, the symptoms appear to be corruption of OpenGL
> > state. The VMD GUI menus all work for me, but the OpenGL window is
> > not displaying correctly. I have gone through a number of state
> > changes and gotten it to partially recover, but that seems to be the
> > root of the problem I'm seeing in all of the versions I've tested so
> far.
> >
> > Cheers,
> > John
> >
> > On Tue, Feb 09, 2010 at 09:24:14AM -0500, Axel Kohlmeyer wrote:
> > > On Tue, 2010-02-09 at 09:47 +0000, Christopher McLean wrote:
> > >
> > > chris,
> > >
> > > > Thanks for the feedback Axel,
> > > >
> > > >
> > > >
> > > > The user is on:
> > > >
> > > > * Kernel: 2.6.31-19-generic-pae (i686)
> > > >
> > > > * Distro: Ubuntu 9.10
> > > >
> > > > * VMD for LINUX, version 1.8.7 (August 1, 2009)
> > >
> > > ok. so that means it is not only one architecture (i run on x86_64)
> > > and one kind of linux.
> > >
> > > >
> > > > It is not possible at this moment to move this user to another
> > > > environment, although we could test dev builds on this machine if
> > >
> > > i already tested the latest development sources. it has to be
> > > something that was broken during the development of 1.8.7.
> > > that was a very long development cycle and some changes to how
> > > molecules are initialized were made.
> > >
> > > it might be useful to install the previous version of vmd as
> > > vmd-1.8.6 in parallel to the current version (which is still
> > > recommended to use for everything else) so that your user can keep
> > > working (that is what i often do in such cases).
> > >
> > > > needed. Should a bug report be filed for this or is this list
> > > > monitored by the devs? Am happy to provide any further
> information
> > > > as needed
> > >
> > > for the most part there is just _the_ "dev", john stone, and he is
> > > very good at keeping track of what is going on.
> > > he is also very busy. it looks like a very odd bug, perhaps related
> > > to some internal state. outside of him there are very few people
> > > that have looked into the intestines of VMD deep enough and are
> > > still actively working on it.
> > >
> > > i have uploaded a viewmaster session file to the VMD public biofs
> > > under testfiles/akohlmey/viewmaster-bug/
> > > that will hopefully make it easier to track it down.
> > >
> > > cheers,
> > > axel.
> > >
> > >
> > > >
> > > >
> > > > Regards
> > > >
> > > >
> > > >
> > > > Chris
> > > >
> > > >
> > > >
> > > > > -----Original Message-----
> > > >
> > > > > From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> > > >
> > > > > Sent: 08 February 2010 17:48
> > > >
> > > > > To: Christopher McLean
> > > >
> > > > > Cc: 'vmd-l_at_ks.uiuc.edu'
> > > >
> > > > > Subject: Re: vmd-l: Blank thumbnails and non-working snapshots
> > > >
> > > > >
> > > >
> > > > > On Mon, 2010-02-08 at 15:55 +0000, Christopher McLean wrote:
> > > >
> > > > > > Hi,
> > > >
> > > > >
> > > >
> > > > > hi chris,
> > > >
> > > > >
> > > >
> > > > > > One of our students is having issues with the ViewMaster
> plugin.
> > > > When
> > > >
> > > > > > snapshots are taken, and the project saved, upon reloading,
> > > > > > the
> > > >
> > > > > > thumbnails are blank and clicking one of the thumbnails does
> > > > > > not
> > > >
> > > > > > reload the view. The thumbnails look fine upon creation
> before
> > > >
> > > > > > save/reload.
> > > >
> > > > >
> > > >
> > > > > confirmed. i see the same thing here on a fedora 12 x86_64
> > > > > machine
> > > >
> > > > > with the current development code. after reloading the state,
> > > > > some
> > > >
> > > > > more things seem to be broken. like new representations can
> only
> > > > > be
> > > >
> > > > > created for lines and points.
> > > >
> > > > >
> > > >
> > > > > unfortunately, i cannot give any pointers as to how to resolve
> this.
> > > >
> > > > > it looks like something deep inside of VMD is going wrong.
> using
> > > >
> > > > > valgrind doesn't show anything unusual.
> > > >
> > > > >
> > > >
> > > > > can you please check what platform your user is using, and
> > > > > perhaps
> > > >
> > > > > have him or her try a different platform? that could provide a
> > > > > hint
> > > >
> > > > > where to look.
> > > >
> > > > >
> > > >
> > > > > thanks,
> > > >
> > > > > axel.
> > > >
> > > > > >
> > > >
> > > > > > Any help or pointers would be appreciated.
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > > > > Regards
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > > > > Chris
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > > > >
> > > >
> > > >
> > >
> > > --
> > > Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational
> > > Molecular Science College of Science and Technology Temple
> > > University, Philadelphia PA, USA.
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> > Institute for Advanced Science and Technology University of Illinois,
> > 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> Institute for Advanced Science and Technology University of Illinois,
> 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
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