VMD-L Mailing List
From: Michael Patzschke (patzsc21_at_hzdr.de)
Date: Fri Feb 13 2015 - 21:02:28 CST
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 “Browse” button in the Molecule File Browser. If one gives
the name of a pdb file (download from pdb.org <http://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
> On 13 Feb 2015, at 18:26, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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.
> John Stone
> 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???
>>> On 12 Feb 2015, at 17:04, John Stone <johns_at_ks.uiuc.edu> wrote:
>>> 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?
>>> John Stone
>>> On Thu, Feb 12, 2015 at 04:08:12PM +0100, Michael Patzschke wrote:
>>>> 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!
>>> 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
> 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