From: Carolyn Phillips (phillicl_at_umich.edu)
Date: Mon Aug 24 2009 - 18:24:36 CDT

That works! I will alias to that in my bashrc file.

Thanks for the help John.

Carolyn

On Aug 24, 2009, at 4:42 PM, John Stone wrote:

>
> Carolyn,
> Can you try running it like this and let me know if that works for
> you?:
> /Applications/VMD 1.8.7.app/Contents/MacOS/startup.command
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Aug 24, 2009 at 12:33:04PM -0400, Carolyn Phillips wrote:
>> 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
>>>
>>>
>
> --
> 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
>
>