VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 12 2010 - 14:13:30 CST

Hi,
  Just FYI, I have changed the VMD startup scripts to include the extra
"-a Terminal" flags to prevent this type of problem from occuring
in the future.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 07, 2010 at 08:02:37AM -0600, Leonardo Trabuco wrote:
> Dear Wayne,
>
> On Thu, Jan 7, 2010 at 6:44 AM, Wayne Dawson <dawson_at_bi.a.u-tokyo.ac.jp> wrote:
> >
> >> I think VMD is assuming that you are using the default Terminal
> >> application for opening files with the extension ".command". If you've
> >> overridden this and set NetBeans to open .command files, and if NetBeans
> >> does not behave like Terminal does (ie. it should run the contents of the
> >> .command file as a shell script), then it probably won't launch VMD
> >> correctly.
> >>
> >> If that is the problem, you can fix it by creating somefile.command (it
> >> can be empty), then do a File:Get info on it, and set the default
> >> application for opening the file to Terminal, and tell it to apply that
> >> preference to all files with the extension.
> >>
> > Thank you for the suggestions.
> >
> >
> > I finally found a related post at
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4954.html
> >
> >
> > It seems that "open" is rather unreliable.  They really should have a flag
> > for opening a terminal, like what probably happened for the text editor in
> > the post above, but they don't.
>
> "open" does have such a flag, actually. Try "open -a Terminal".
>
> Cheers,
> Leo
>
> > The only application in the entire /Applications and $HOME directory with
> > the name startup.command is there inside of "VMD 1.8.7app".
> >
> > What I found works ok is to open a terminal and start vmd as an alias
> >
> >> cat .bash_profile
> > #  .....
> > alias vmd="/Applications/VMD 1.8.7.app/Contents/MacOS/startup.command"
> >
> >
> > launch  "Terminal.app" and type "vmd".  That works at least.
> > Wayne
> >
> >>
> >
> > --
> > -----------------------------------------------------------
> > Bioinformation Engineering Laboratory
> > Building 6
> > Department of Biotechnology
> > Division of Agriculture
> > Graduate School of Agricultural and Life Sciences
> > The University of Tokyo Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657
> >
> > TEL          (+81)-3-5841-5449
> > cellphone    (+81)-090-5312-9325
> >
> >
>
>
>
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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