VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 31 2014 - 14:51:38 CDT

Hi,
  Again, I'd have to say that this currently sounds like a video driver
bug as other people running Yosemite with different graphics chips/drivers
have not reported this problem, or at least not yet.... I always advise
VMD users against being first-in-line to update to new OS versions,
particularly in the case of MacOS X, because they often break the video
drivers in the early versions of new OS releases. At present I don't
have any suggestion for a workaround, but I would suggest looking on
google to see if users of other high-end OpenGL apps have encountered
similar bugs on similar hardware. If anyone has further comments or
has observed this or other problems on Yosemite, I'd love to hear about it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 31, 2014 at 12:32:26PM -0400, Nick Fisher wrote:
> Hi John
> Thanks for your reply.
> On reading a PDB file the spinning VMD logo freezes, although the program
> is otherwise responsive (i.e. the menu items in the VMD main window etc.
> still work). If I resize the OpenGL display with the frozen logo it
> reverts to black, and the VMD logo is lost.
> Changing the mouse focus whilst the logo is spinning doesn't seem to cause
> any problems. Similarly, resizing the window with the logo spinning seems
> to be fine.
> This problem is present on release versions of VMD 1.8.6 to 1.9.2.
> Cheers,
> Nick
> ---------------------------------
> Nick Fisher, Ph.D.
> MSU-DOE Plant Research Laboratory
> Michigan State University
> Plant Biology Laboratories
> 612 Wilson Road, S-234
> East Lansing, MI 48824
> United States
>
> email: [1]nefisher_at_msu.edu
> tel: 517-432-0071 (lab)
>
> On 31 Oct 2014, at 12:22, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
> Hi,
> This sounds like a new video driver bug of some kind,
> particularly since your problems started after you upgraded to Yosemite.
>
> What happens if you try resizing the display window, or you switch
> mouse focus to a different application and then switch back to VMD?
>
> Cheers,
> John Stone
> [3]vmd_at_ks.uiuc.edu
>
> On Fri, Oct 31, 2014 at 11:51:09AM -0400, Nick Fisher wrote:
>
> The OpenGL display window of VMD 1.9.1 (non-CUDA) is freezing
> immediately
> after loading a set of PDB coordinates in a fresh install of OS X
> 10.10
>
> Ia**m using a late-2012 Mac Mini (8 Gb RAM, 2.5 GHz i5, Intel HD
> 4000
> graphics). The spinning VMD logo freezes, and the molecule is not
> displayed. Herea**s the console log (note that the program does not
> crash,
> it is just unusable):
>
> Info) VMD for MACOSXX86, version 1.9.1 (February 4, 2012)
> Info)
> [1][4]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to
> [2][5]vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
> Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048),
> Multitexture
> (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Applications/VMD
> 1.9.1.app/Contents/vmd/plugins/MACOSXX86/molfile
> vmd > Info) Using plugin pdb for structure file /Applications/Bowman
> bc1
> /1SQP.pdb
> Info) Using plugin pdb for coordinates from file
> /Applications/Bowman bc1
> /1SQP.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 17274
> Info) Bonds: 17481
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0
> Impropertypes: 0
> Info) Residues: 2329
> Info) Waters: 215
> Warning) Unusual bond between residues: 83 (protein) and 382 (none)
> Warning) Unusual bond between residues: 37 (protein) and 243 (none)
> Info) Segments: 1
> Info) Fragments: 236 Protein: 11 Nucleic: 0
> Info) Finished with coordinate file /Applications/Bowman bc1
> /1SQP.pdb.
>
> References
>
> Visible links
> 1. [6]http://www.ks.uiuc.edu/Research/vmd/
> 2. [7]mailto:vmd_at_ks.uiuc.edu
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [8]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [9]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:nefisher_at_msu.edu
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. http://www.ks.uiuc.edu/Research/vmd/
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. http://www.ks.uiuc.edu/~johns/
> 9. 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/