VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 13 2015 - 11:26:50 CST

Michael,
  On the new machine, what specific Yosemite version number are you running?
This sounds to me like a Yosemite issue (again) rather than a VMD issue,
but having more system details is helpful either way.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 12, 2015 at 05:48:30PM +0100, Michael Patzschke wrote:
> Hello John,
>
> Thank you for your fast reply. My apologies for being a bit vague
> in my last mail:
>
> Both the 2012 and the 2014 Mac run the same MacOS. On the old
> machine the cube files still load perfectly and everything else works
> as expected. On the new machine the OpenGL window freezes.
> This is true for both for 1.9.2. and 1.9.1.
>
> The cube files were generated with different codes (i.e. MultiWFN,
> nciplot and such) none of them works. The new Mac has 16GB of
> memory and about 6 are free. It uses and Intel Iris Pro card with
> 1,5 GB dedicated RAM.
>
> I have tried everything now and the only thing that does work on the
> new machine is opening a pdb file over the net. Everything else fails.
> I have been using Macs for a long time and I feel rather stupid now.
> I am grateful for any advice???
>
> Regards,
> Michael
>
>
> > On 12 Feb 2015, at 17:04, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Michael,
> > It's possibly a MacOS X issue if you have recently upgraded your machines
> > to Yosemite. That said, it's worth asking more details about the cube
> > files also. So, the problem only occurs when loading cube files, but
> > everything else is fine? We haven't changed anything terribly significant
> > in the Gaussian cube file reader recently. Axel taught it to recognize cube
> > files from g09 rev d.01 back in 2013, but that's the only change since 2009.
> > Perhaps your cube files are a particular variant of the format that the
> > VMD plugin doesn't handle yet? What Gaussian rev generated them?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Feb 12, 2015 at 04:08:12PM +0100, Michael Patzschke wrote:
> >> Hi,
> >>
> >> This is most probably a Mac issue, but I would appreciate any advice.
> >> I have been using VMD for years on my MacBook Air (2012). Now I have
> >> a new MacBook Pro (mid 2014) and to my dismay, loading gaussian cube
> >> files does not work any more.
> >>
> >> I can load pdb files and other structural files and manipulate them, but as
> >> soon as I start loading cube files, the OpenGL Display window just freezes.
> >> This happens with both vmd 1.9.2 and 1.9.1
> >>
> >> Both Macs have a very similar setup (Quartz and MacPorts installed with quite
> >> a number of graphical routine ports installed, but I highly doubt, that they would
> >> interfere with vmd)
> >>
> >> I would very much appreciate any help or hints how to solve this problem!
> >>
> >> Regards,
> >> Michael
> >
> > --
> > 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/