VMD-L Mailing List

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Mon Aug 24 2009 - 21:49:10 CDT

VMD 1.8.7 also hangs for me sometimes on Mac OSX 10.5.8. I thought it might
be a memory issue, even with my 4 GB of memory on 2.0 GHz Core 2 Duo.
Josh

------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
------------------------------------------------

On Tue, Aug 25, 2009 at 2:24 AM, Carolyn Phillips <phillicl_at_umich.edu>wrote:

> 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
>>
>>
>>
>