VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 24 2009 - 15:42:49 CDT

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