I'd love to give it a try. What do I do with the code you have below?
G
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
>> >>>>>
>> >>>>>
------------------------------------------------------------------------------
>> >>>>> FREE DOWNLOAD - uberSVN with Social Coding for Subversion.
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>> >>>>> http://p.sf.net/sfu/wandisco-dev2dev
>
--
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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