VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Tue Aug 25 2009 - 12:53:02 CDT

I found the same trick on my Mac pro core 2 duo.. if you leave VMD to run
for a while without any click it works. But if it hangs I open the
tkconsole from the
VMD terminal and it works again.

Best
Daniel Aguayo

On Tue, Aug 25, 2009 at 1:00 PM, Robert Brunner<rbrunner_at_illinois.edu> wrote:
> The workaround I've found on my PPC Mac is to not click on any other
> application until the VMD icon is done bouncing. If you leave VMD in the
> foreground until startup is complete, it seems to make FLTK happy.
>
> I have not tested this on an Intel Mac.
>
> Robert
>
> On Aug 25, 2009, at 10:34 AM, John Stone wrote:
>
>>
>> Hi,
>>  It's not a memory issue (we have it on our macs here too).
>> This is some kind of GUI event handling problem either in Tcl/Tk, or in
>> FLTK.
>> I haven't tracked down which library is at fault yet, but my guess
>> is that is an FLTK problem.  I will be upgrading the next version of
>> VMD to the latest FLTK, and hopefully this will cure the problem.
>> If not, then I'll have to dig into it further.
>>
>> Cheers,
>>  John Stone
>>  vmd_at_ks.uiuc.edu
>>
>> On Tue, Aug 25, 2009 at 05:49:10AM +0300, Joshua D. Moore wrote:
>>>
>>>  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
>>
>> --
>> 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
>
> 

-- 
saludos desde el fin del mundo