VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 10 2015 - 16:06:02 CDT

Hi,
  In case you didn't see my other posting last night,
I recently exchanged many emails with Adrian Roitberg who had
the same Mac problem, and it seems that we have found a short-term
workaround for the MacOS X Yosemite 10.10.2 update problems that
have recently cropped up on certain varieties of Mac laptops.
The solution is to set an environment variable to tell VMD not to
use the MacOS-provided file browser window, and to instead use the
FLTK-based file chooser. This is done by setting the environment variable
"VMDFILECHOOSER" to the value "FLTK". This can be done in VMD itself
in the text console, in the user's .vmdrc file, in the global .vmdrc
file in the VMD.app bundle, or by setting the environment variable in the
user's Unix shell .bashrc, etc.

To set the variable in VMD or .vmdrc etc, run this command:
     set env(VMDFILECHOOSER) FLTK

To set the variable in bash, add this to .bashrc etc:
  VMDFILECHOOSER=FLTK
  export VMDFILECHOOSER

After the environment variable is set, VMD will use the alternative
file selector window in the graphical interface, and this should prevent
the problems you've been encountering.

Let me know if the workaround is successful for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 14, 2015 at 04:02:28AM +0100, Michael Patzschke wrote:
> John,
> Thank you very much for your efforts! I have to apologise, when I first
> started this thread I had limited internet access. Now I have searched
> a bit more and it seems that man yosemite users experience this problem.
> There is actually a solution, although one that implies, that the problem
> might not be OpenGL related. The problem appears always and only if
> one uses the â**Browseâ** button in the Molecule File Browser. If one
> gives
> the name of a pdb file (download from [1]pdb.org) or the complete path of
> the local file one wants to open everything is fine. it is also no problem
> to
> start vmd directly with a filename.
> Also to answer your question on the os version:
> System Version: OS X 10.10.2 (14C109)
> Kernel Version: Darwin 14.1.0
> And the machine:
> Model Identifier: MacBookPro11,3
> Processor Name: Intel Core i7
> Processor Speed: 2,5 GHz
> Number of Processors: 1
> Total Number of Cores: 4
> L2 Cache (per Core): 256 KB
> L3 Cache: 6 MB
> Memory: 16 GB
> Thanks again,
> Michael
>
> On 13 Feb 2015, at 18:26, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
> 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
> [3]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 <[4]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
> [5]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
> [6]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [7]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
> [8]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [9]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://pdb.org/
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. http://www.ks.uiuc.edu/~johns/
> 7. http://www.ks.uiuc.edu/Research/vmd/
> 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/