From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 31 2014 - 11:22:29 CDT

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
  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]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [2]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. http://www.ks.uiuc.edu/Research/vmd/
> 2. 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/