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 Millhauser
> >>>> Department of Chemistry & Biochemistry
> >>>> UC Santa Cruz
> >>>> Santa Cruz, CA 95064
> >>>>
> >>>> 831 459 2176 voice
> >>>> 831 459 2935 fax
> >>>> 831 566 3337 cell
> >>>>
> >>>> [email protected]
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> >>>> http://chemistry.ucsc.edu/~glennm
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> ------------------------------------------------------------------------------
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> >>
> >>
> >>
> >> Glenn Millhauser
> >> Department of Chemistry & Biochemistry
> >> UC Santa Cruz
> >> Santa Cruz, CA 95064
> >>
> >> 831 459 2176 voice
> >> 831 459 2935 fax
> >> 831 566 3337 cell
> >>
> >> [email protected]
> >>
> >> http://chemistry.ucsc.edu/~glennm
> >>
> >>
> >>
> >>
>
>
>
> Glenn Millhauser
> Department of Chemistry & Biochemistry
> UC Santa Cruz
> Santa Cruz, CA 95064
>
> 831 459 2176 voice
> 831 459 2935 fax
> 831 566 3337 cell
>
> [email protected]
>
> http://chemistry.ucsc.edu/~glennm
>
>
>
>
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