VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 09 2010 - 10:07:31 CST

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