From: Gabrielle Garcia (gm.rodriguez08_at_gmail.com)
Date: Wed May 06 2015 - 15:58:43 CDT

Hi John,

Thank you for the info… changing the environment variable to FLTK seemed to help… the trajectory frames began loading in openGL and then crashed.. So it may or may not be an issue separate from Mac OS X glitch..
> On May 6, 2015, at 1:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> This problem is starting to sound suspiciously like the
> recent MacOS X Yosemite 10.10.2 update... Below I'm pasting
> in the note I sent to people that have fallen victim to graphics
> issues of various kinds after recent Apple MacOS Yosemite software updates:
>
> I recently exchanged many emails with Adrian Roitberg who had
> the same Mac Yosemite 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 Wed, May 06, 2015 at 04:31:18PM -0400, Axel Kohlmeyer wrote:
>> On Wed, May 6, 2015 at 4:28 PM, Gabrielle Garcia
>> <gm.rodriguez08_at_gmail.com> wrote:
>>> There are no error messages in the VMD console, nor is there any indication
>>> that VMD was not able to load my trajectory.
>>> All atoms were read and all frames were loaded.. The OpenGL frame freezes
>>> with the VMD logo (instead of it bouncing around). I will wait to see if
>>> anyone else has had a similar experience.
>>
>> that sounds almost like a bug in the OpenGL driver. apple doesn't have
>> a good track record recently with the graphics drivers shipped with
>> macosx.
>>
>> axel.
>>
>>>
>>> Thanks,
>>>
>>> Gabrielle
>>>
>>> On May 6, 2015, at 1:17 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>>
>>> On Wed, May 6, 2015 at 4:12 PM, Gabrielle Garcia
>>> <gm.rodriguez08_at_gmail.com> wrote:
>>>
>>> Hi Dr. Kohlmeyer,
>>>
>>> Thank you for your response.. Yes, I do have netCDF capability. (positive
>>> number returned).
>>> However, my when my trajectory loads into the VMD console, there is nothing
>>> in the openGL screen. It is just the VMD logo on display.
>>> When I open the same trajectory on my Linux machine in lab, it comes up and
>>> loads all frames immediately.
>>>
>>> I???m not sure if there???s a specific setting to look for.
>>>
>>>
>>> i don't know either. there either has to be some error message
>>> somewhere or you should at the very least see in the VMD Main window
>>> information about the trajectory file and how many frames were loaded.
>>> i don't know the details of all the steps you perform and whether all
>>> library and software versions are comparable to your linux version.
>>>
>>> perhaps your files were not properly transferred (as text and not
>>> binary files) or got otherwise corrupted?
>>>
>>> axel.
>>>
>>>
>>>
>>> Gabrielle
>>>
>>>
>>> On May 6, 2015, at 12:53 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>>
>>> On Wed, May 6, 2015 at 2:44 PM, Gabrielle Garcia
>>> <gm.rodriguez08_at_gmail.com> wrote:
>>>
>>> Hi everyone,
>>>
>>> I have VMD 1.9.2 (without CUDA) downloaded on my MacBook Pro (w/Retina
>>> display).
>>> I am having trouble bringing up my .nc trajectory in VMD. I confirmed that
>>> the files work with my linux machine at work.. but they won???t display on my
>>> MacBook. Is there a way to visualize my netCDF trajectories on my MacBook
>>> even without GPU?
>>>
>>>
>>> netCDF support is independent of GPU support. support for netCDF
>>> format data requires that a plugin is installed which requires support
>>> from an external library. not all external library work equally well
>>> on all platforms and hence some plugins and features in VMD are not
>>> available on all platforms.
>>>
>>> you can easily check whether suitable plugin support is available by
>>> running the following command on the VMD console:
>>>
>>> lsearch -index 1 [plugin list] netcdf
>>>
>>> if this returns a positive number, then netcdf support is available,
>>> if it returns -1 then the plugin has not been compiled/packages for
>>> that specific VMD version.
>>>
>>> axel.
>>>
>>>
>>> Thanks,
>>>
>>> Gabrielle
>>>
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> 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/