VMD-L Mailing List

From: Carolyn Phillips (phillicl_at_umich.edu)
Date: Mon Aug 24 2009 - 11:33:04 CDT

Hi John,

To date it has happened every time.

Here are some observations. The hanging occurs whether I load a
molecule file or not. The hanging is associated with the GUI and not
with the command line, which I can still use to exit out of the program.

If I changed to the directory "/Applications/VMD\ 1.8.7.app/Contents/
vmd/" and then run it with "./vmd_MACOSXX86" I get precisely the same
behavior.

I can get VMD 1.8.7 to work successfully by using the Launcher
instead, but then I have use the GUI browser to open my files, and
can't just open them straight from the command line.

-Carolyn

On Aug 23, 2009, at 10:32 PM, John Stone wrote:

> Hi Carolyn,
> Does this occur repeatably, every single time, or is it intermittent?
> (I have no mac to test on at home)
>
> I didn't change anything Mac-specific in the VMD startup code for
> VMD 1.8.7, but there seem to be a few intermittent GUI event handling
> issues associated with Tcl/Tk 8.5.6 that have cropped up that affect
> VMD. I'm wondering if this is one of those, or if it's something
> entirely different.
>
> Do you get the same behavior if you change your working directory
> to "/Applications/VMD\ 1.8.7.app/Contents/vmd/" and then run it with
> ./vmd_MACOSXX86 or does it behave in the same way? (I'm wondering
> about shared library dependencies being an issue...)
>
> Run those tests and let me know what you find. Depending on the
> results, I may have ideas for workarounds for you.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Sun, Aug 23, 2009 at 04:13:40PM -0400, Carolyn Phillips wrote:
>> Hello, I am using a Mac OSX 10.5.8 and just downloaded the newest
>> version of VMD 1.8.7.
>>
>> With VMD 1.8.6, I could use vmd from my command line in terminal by
>> simply typing
>>
>> /Applications/VMD\ 1.8.6.app/Contents/vmd/vmd_MACOSXX86 MyFiles.mol2
>>
>> But the same line using VMD 1.8.7 (i.e.
>>
>> /Applications/VMD\ 1.8.7.app/Contents/vmd/vmd_MACOSXX86 MyFiles.mol2
>>
>> )
>>
>> successfully opens the file but then VMD hangs... (i.e. mac's
>> spinning
>> pinwheel of death.)
>>
>> How can I recover command-line use of VMD 1.8.7 on a Mac?
>>
>> Thanks,
>> Carolyn Phillips
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>