On Sat, Aug 13, 2011 at 01:45:29PM -0700, Glenn Millhauser wrote:
> I'd love to give it a try. What do I do with the code you have below?
> G
>
Glenn,
On Lion, the packaging for mesa-libglw and molmol on fink tracking should
work...
http://sourceforge.net/tracker/?func=detail&aid=3391210&group_id=17203&atid=414256
http://sourceforge.net/tracker/?func=detail&aid=3391212&group_id=17203&atid=414256
Jack
> On Saturday, August 13, 2011, Jack Howarth <howa...@bromo.med.uc.edu> wrote:
> > On Sat, Aug 13, 2011 at 12:22:14PM -0700, Glenn Millhauser wrote:
> >> Okay -- I'll check in periodically. This is unfortunate. Molmol is
> dated, but there are a few things that it does really well, much better than
> most of the current software. Fingers crossed for a fix.
> >> all the best,
> >> g
> >
> > Glenn,
> > Actually, I think I have a workaround...
> >
> > --- /sw/bin/molmol.sav 2011-08-13 16:32:28.000000000 -0400
> > +++ /sw/bin/molmol 2011-08-13 16:38:14.000000000 -0400
> > @@ -161,8 +161,8 @@
> > esac
> > fi
> >
> > -if [ "$input" = "-" -o -n "$nograph" ]; then
> > +#if [ "$input" = "-" -o -n "$nograph" ]; then
> > echo "LineBond solid 1 " >>| $startmacro ;
> /sw/share/molmol/src/main/molmol $xopt
> > -else
> > - echo "LineBond solid 1 " >>| $startmacro ;
> /sw/share/molmol/src/main/molmol $xopt < /dev/null
> > -fi
> > +#else
> > +# echo "LineBond solid 1 " >>| $startmacro ;
> /sw/share/molmol/src/main/molmol $xopt < /dev/null
> > +#fi
> >
> > For some reason the extra redirection from /dev/null seems to break under
> Lion.
> > Jack
> >
> >>
> >> On Aug 13, 2011, at 10:51 AM, Jack Howarth wrote:
> >>
> >> > On Sat, Aug 13, 2011 at 10:37:54AM -0700, Glenn Millhauser wrote:
> >> >> Thank you, Jack. So then even if I install Macports, molmol will not
> run -- am I right on this? I guess, then, molmol is dead for the time
> being. Is there any way for me to follow the Xquartz progress to see when
> things are updated, thus enabling molmol, once again? My understanding of
> all this stuff is not deep -- I really appreciate the information/advice.
> >> >> thanks,
> >> >> glenn
> >> >>
> >> >
> >> > Glenn,
> >> > The Xquartz development mailing list is archived at
> http://lists.macosforge.org/pipermail/xquartz-dev/.
> >> > The MacPorts xorg packages are more or less synchronized with those
> releases. In MacPorts, they build and link
> >> > against those xorg packages in /opt/local but run with the Xserver from
> either the system X11 or Xquartz.
> >> > I've opened https://svn.macports.org/ticket/30746 but wouldn't get my
> hopes up for a quick fix since we never
> >> > determined what xorg change eliminated the previous instance of this
> widget issue in MacPorts. Also if it
> >> > is a fixable flaw in X11/Xquartz, you'll have to wait for a fixed
> release of either the system X11 or Xquartz.
> >> > Jack
> >> >
> >> >>
> >> >> On Aug 13, 2011, at 10:02 AM, Jack Howarth wrote:
> >> >>
> >> >>> On Sat, Aug 13, 2011 at 09:49:09AM -0700, Glenn Millhauser wrote:
> >> >>>> So does this mean that we have no chance of getting molmol running
> again? Jack, if I understand correctly, you tried to build a fresh molmol
> in Lion with the latest Fink distribution, but the windows still do not
> display properly. Is there anything that you recommend that I try? If I
> understand Alexander's suggestion, I could install the latest Fink and then
> try "fink rebuild molmol." Any chance of that solving the problem?
> >> >>>> thanks,
> >> >>>> glenn
> >> >>>
> >> >>> Glenn,
> >> >>> What is means is that the issue has to be punted to the Xquartz
> developers. This is one reason
> >> >>> I ported molmol/pymol to MacPorts was so that those packages could be
> tested against the upcoming
> >> >>> Xquartz releases (which appear in the form of their xorg related
> packages). Either the problem
> >> >>> was previously fixed and then broken again or it just went latent for
> awhile. This was a major
> >> >>> concern of mine about the absence of Xquartz support in fink (that we
> would be blindsided with
> >> >>> X11 issues on new system releases that adopted the work from
> Xquartz).
> >> >>> Jack
> >> >>>
> >> >>>>
> >> >>>>
> >> >>>> On Aug 13, 2011, at 7:54 AM, Jack Howarth wrote:
> >> >>>>
> >> >>>>> As far as I have been able to tell the breakage seems to be
> introduced with the
> >> >>>>> new X11 in Lion. The molmol program built either under SL and run
> under Lion or
> >> >>>>> built under Lion fails to display the widgets or menus in its
> windows. The current
> >> >>>>> bahavior looks a lot like something we saw on MacPorts
> previously...
> >> >>>>>
> >> >>>>> https://trac.macports.org/ticket/21835
> >> >>>>>
> >> >>>>> Perhaps the problem resurfaced again. Unfortunately it was never
> determined exactly
> >> >>>>> what change to the xorg packages solved the problem.
> >> >>>>> Jack
> >> >>>>>
> >> >>>>>
> ------------------------------------------------------------------------------
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> >
>
> --
> Glenn L. Millhauser
> Chemistry
> UCSC
> voice (831) 459-2176
> cell (831) 566-3337
>
> gle...@ucsc.edu
>
> http://chemistry.ucsc.edu/~glennm
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